From 9e80d4683d657942410489dc92683c1619ed252e Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 10 Jul 2023 14:30:40 +0200 Subject: [PATCH] add config option in doc of all tools --- bin/agat_convert_bed2gff.pl | 2 +- bin/agat_convert_embl2gff.pl | 2 +- bin/agat_convert_genscan2gff.pl | 2 +- bin/agat_convert_mfannot2gff.pl | 2 +- bin/agat_convert_minimap2_bam2gff.pl | 2 +- bin/agat_convert_sp_gff2bed.pl | 2 +- bin/agat_convert_sp_gff2gtf.pl | 2 +- bin/agat_convert_sp_gff2tsv.pl | 2 +- bin/agat_convert_sp_gff2zff.pl | 2 +- bin/agat_convert_sp_gxf2gxf.pl | 2 +- bin/agat_sp_Prokka_inferNameFromAttributes.pl | 2 +- bin/agat_sp_add_attribute_shortest_exon_size.pl | 2 +- bin/agat_sp_add_attribute_shortest_intron_size.pl | 2 +- bin/agat_sp_add_introns.pl | 2 +- bin/agat_sp_add_start_and_stop.pl | 2 +- bin/agat_sp_alignment_output_style.pl | 2 +- bin/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl | 2 +- bin/agat_sp_compare_two_BUSCOs.pl | 2 +- bin/agat_sp_compare_two_annotations.pl | 2 +- bin/agat_sp_complement_annotations.pl | 2 +- bin/agat_sp_ensembl_output_style.pl | 2 +- bin/agat_sp_extract_attributes.pl | 2 +- bin/agat_sp_extract_sequences.pl | 2 +- bin/agat_sp_filter_by_ORF_size.pl | 2 +- bin/agat_sp_filter_by_locus_distance.pl | 2 +- bin/agat_sp_filter_by_mrnaBlastValue.pl | 2 +- bin/agat_sp_filter_feature_by_attribute_presence.pl | 2 +- bin/agat_sp_filter_feature_by_attribute_value.pl | 2 +- bin/agat_sp_filter_feature_from_keep_list.pl | 2 +- bin/agat_sp_filter_feature_from_kill_list.pl | 2 +- bin/agat_sp_filter_gene_by_intron_numbers.pl | 2 +- bin/agat_sp_filter_gene_by_length.pl | 2 +- bin/agat_sp_filter_incomplete_gene_coding_models.pl | 2 +- bin/agat_sp_filter_record_by_coordinates.pl | 2 +- bin/agat_sp_fix_cds_phases.pl | 2 +- bin/agat_sp_fix_features_locations_duplicated.pl | 2 +- bin/agat_sp_fix_fusion.pl | 2 +- bin/agat_sp_fix_longest_ORF.pl | 2 +- bin/agat_sp_fix_overlaping_genes.pl | 2 +- bin/agat_sp_fix_small_exon_from_extremities.pl | 2 +- bin/agat_sp_flag_premature_stop_codons.pl | 2 +- bin/agat_sp_flag_short_introns.pl | 2 +- bin/agat_sp_functional_statistics.pl | 2 +- bin/agat_sp_keep_longest_isoform.pl | 2 +- bin/agat_sp_kraken_assess_liftover.pl | 2 +- bin/agat_sp_list_short_introns.pl | 2 +- bin/agat_sp_load_function_from_protein_align.pl | 2 +- bin/agat_sp_manage_IDs.pl | 2 +- bin/agat_sp_manage_UTRs.pl | 2 +- bin/agat_sp_manage_attributes.pl | 2 +- bin/agat_sp_manage_functional_annotation.pl | 2 +- bin/agat_sp_manage_introns.pl | 2 +- bin/agat_sp_merge_annotations.pl | 2 +- bin/agat_sp_prokka_fix_fragmented_gene_annotations.pl | 2 +- bin/agat_sp_sensitivity_specificity.pl | 2 +- bin/agat_sp_separate_by_record_type.pl | 2 +- bin/agat_sp_statistics.pl | 2 +- bin/agat_sp_webApollo_compliant.pl | 2 +- bin/agat_sq_add_attributes_from_tsv.pl | 2 +- bin/agat_sq_add_hash_tag.pl | 2 +- bin/agat_sq_add_locus_tag.pl | 2 +- bin/agat_sq_count_attributes.pl | 2 +- bin/agat_sq_filter_feature_from_fasta.pl | 2 +- bin/agat_sq_list_attributes.pl | 2 +- bin/agat_sq_manage_IDs.pl | 2 +- bin/agat_sq_manage_attributes.pl | 2 +- bin/agat_sq_mask.pl | 2 +- bin/agat_sq_remove_redundant_entries.pl | 2 +- bin/agat_sq_rename_seqid.pl | 2 +- bin/agat_sq_repeats_analyzer.pl | 2 +- bin/agat_sq_reverse_complement.pl | 2 +- bin/agat_sq_rfam_analyzer.pl | 2 +- bin/agat_sq_split.pl | 2 +- bin/agat_sq_stat_basic.pl | 2 +- docs/tools/agat_convert_bed2gff.md | 6 ++++++ docs/tools/agat_convert_embl2gff.md | 6 ++++++ docs/tools/agat_convert_genscan2gff.md | 6 ++++++ docs/tools/agat_convert_mfannot2gff.md | 6 ++++++ docs/tools/agat_convert_minimap2_bam2gff.md | 6 ++++++ docs/tools/agat_convert_sp_gff2bed.md | 6 ++++++ docs/tools/agat_convert_sp_gff2gtf.md | 6 ++++++ docs/tools/agat_convert_sp_gff2tsv.md | 6 ++++++ docs/tools/agat_convert_sp_gff2zff.md | 6 ++++++ docs/tools/agat_convert_sp_gxf2gxf.md | 6 ++++++ docs/tools/agat_sp_Prokka_inferNameFromAttributes.md | 6 ++++++ docs/tools/agat_sp_add_attribute_shortest_exon_size.md | 6 ++++++ docs/tools/agat_sp_add_attribute_shortest_intron_size.md | 6 ++++++ docs/tools/agat_sp_add_introns.md | 6 ++++++ docs/tools/agat_sp_add_start_and_stop.md | 6 ++++++ docs/tools/agat_sp_alignment_output_style.md | 6 ++++++ .../agat_sp_clipN_seqExtremities_and_fixCoordinates.md | 6 ++++++ docs/tools/agat_sp_compare_two_BUSCOs.md | 6 ++++++ docs/tools/agat_sp_compare_two_annotations.md | 6 ++++++ docs/tools/agat_sp_complement_annotations.md | 6 ++++++ docs/tools/agat_sp_ensembl_output_style.md | 6 ++++++ docs/tools/agat_sp_extract_attributes.md | 6 ++++++ docs/tools/agat_sp_extract_sequences.md | 6 ++++++ docs/tools/agat_sp_filter_by_ORF_size.md | 6 ++++++ docs/tools/agat_sp_filter_by_locus_distance.md | 6 ++++++ docs/tools/agat_sp_filter_by_mrnaBlastValue.md | 6 ++++++ .../tools/agat_sp_filter_feature_by_attribute_presence.md | 6 ++++++ docs/tools/agat_sp_filter_feature_by_attribute_value.md | 6 ++++++ docs/tools/agat_sp_filter_feature_from_keep_list.md | 6 ++++++ docs/tools/agat_sp_filter_feature_from_kill_list.md | 6 ++++++ docs/tools/agat_sp_filter_gene_by_intron_numbers.md | 6 ++++++ docs/tools/agat_sp_filter_gene_by_length.md | 6 ++++++ .../tools/agat_sp_filter_incomplete_gene_coding_models.md | 6 ++++++ docs/tools/agat_sp_filter_record_by_coordinates.md | 8 +++++++- docs/tools/agat_sp_fix_cds_phases.md | 6 ++++++ docs/tools/agat_sp_fix_features_locations_duplicated.md | 6 ++++++ docs/tools/agat_sp_fix_fusion.md | 6 ++++++ docs/tools/agat_sp_fix_longest_ORF.md | 6 ++++++ docs/tools/agat_sp_fix_overlaping_genes.md | 6 ++++++ docs/tools/agat_sp_fix_small_exon_from_extremities.md | 6 ++++++ docs/tools/agat_sp_flag_premature_stop_codons.md | 6 ++++++ docs/tools/agat_sp_flag_short_introns.md | 6 ++++++ docs/tools/agat_sp_functional_statistics.md | 6 ++++++ docs/tools/agat_sp_keep_longest_isoform.md | 6 ++++++ docs/tools/agat_sp_kraken_assess_liftover.md | 6 ++++++ docs/tools/agat_sp_list_short_introns.md | 6 ++++++ docs/tools/agat_sp_load_function_from_protein_align.md | 6 ++++++ docs/tools/agat_sp_manage_IDs.md | 6 ++++++ docs/tools/agat_sp_manage_UTRs.md | 6 ++++++ docs/tools/agat_sp_manage_attributes.md | 6 ++++++ docs/tools/agat_sp_manage_functional_annotation.md | 6 ++++++ docs/tools/agat_sp_manage_introns.md | 6 ++++++ docs/tools/agat_sp_merge_annotations.md | 6 ++++++ .../agat_sp_prokka_fix_fragmented_gene_annotations.md | 6 ++++++ docs/tools/agat_sp_sensitivity_specificity.md | 6 ++++++ docs/tools/agat_sp_separate_by_record_type.md | 6 ++++++ docs/tools/agat_sp_split_by_level2_feature.md | 6 ++++++ docs/tools/agat_sp_statistics.md | 6 ++++++ docs/tools/agat_sp_to_tabulated.md | 6 ++++++ docs/tools/agat_sp_webApollo_compliant.md | 6 ++++++ docs/tools/agat_sq_add_attributes_from_tsv.md | 6 ++++++ docs/tools/agat_sq_add_hash_tag.md | 6 ++++++ docs/tools/agat_sq_add_locus_tag.md | 6 ++++++ docs/tools/agat_sq_count_attributes.md | 6 ++++++ docs/tools/agat_sq_filter_feature_from_fasta.md | 6 ++++++ docs/tools/agat_sq_list_attributes.md | 6 ++++++ docs/tools/agat_sq_manage_ID.md | 6 ++++++ docs/tools/agat_sq_manage_IDs.md | 6 ++++++ docs/tools/agat_sq_manage_attributes.md | 6 ++++++ docs/tools/agat_sq_mask.md | 6 ++++++ docs/tools/agat_sq_remove_redundant_entries.md | 6 ++++++ docs/tools/agat_sq_repeats_analyzer.md | 6 ++++++ docs/tools/agat_sq_reverse_complement.md | 6 ++++++ docs/tools/agat_sq_rfam_analyzer.md | 6 ++++++ docs/tools/agat_sq_split.md | 6 ++++++ docs/tools/agat_sq_stat_basic.md | 6 ++++++ 150 files changed, 531 insertions(+), 75 deletions(-) diff --git a/bin/agat_convert_bed2gff.pl b/bin/agat_convert_bed2gff.pl index b7a87905..4149cb45 100755 --- a/bin/agat_convert_bed2gff.pl +++ b/bin/agat_convert_bed2gff.pl @@ -496,7 +496,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_convert_embl2gff.pl b/bin/agat_convert_embl2gff.pl index 1dc76cc5..720d33f0 100755 --- a/bin/agat_convert_embl2gff.pl +++ b/bin/agat_convert_embl2gff.pl @@ -264,7 +264,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_convert_genscan2gff.pl b/bin/agat_convert_genscan2gff.pl index 6d671d76..6bcfdfa1 100755 --- a/bin/agat_convert_genscan2gff.pl +++ b/bin/agat_convert_genscan2gff.pl @@ -310,7 +310,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_convert_mfannot2gff.pl b/bin/agat_convert_mfannot2gff.pl index 70e26073..e6ebc7b5 100755 --- a/bin/agat_convert_mfannot2gff.pl +++ b/bin/agat_convert_mfannot2gff.pl @@ -464,7 +464,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_convert_minimap2_bam2gff.pl b/bin/agat_convert_minimap2_bam2gff.pl index 881f7df6..44ca42ec 100755 --- a/bin/agat_convert_minimap2_bam2gff.pl +++ b/bin/agat_convert_minimap2_bam2gff.pl @@ -385,7 +385,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_convert_sp_gff2bed.pl b/bin/agat_convert_sp_gff2bed.pl index fb7a6219..f189be6a 100755 --- a/bin/agat_convert_sp_gff2bed.pl +++ b/bin/agat_convert_sp_gff2bed.pl @@ -266,7 +266,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_convert_sp_gff2gtf.pl b/bin/agat_convert_sp_gff2gtf.pl index a7fb1269..b64cd2cb 100755 --- a/bin/agat_convert_sp_gff2gtf.pl +++ b/bin/agat_convert_sp_gff2gtf.pl @@ -142,7 +142,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_convert_sp_gff2tsv.pl b/bin/agat_convert_sp_gff2tsv.pl index 8fad53d6..723ffd97 100755 --- a/bin/agat_convert_sp_gff2tsv.pl +++ b/bin/agat_convert_sp_gff2tsv.pl @@ -273,7 +273,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_convert_sp_gff2zff.pl b/bin/agat_convert_sp_gff2zff.pl index d1c7ce02..bbb95809 100755 --- a/bin/agat_convert_sp_gff2zff.pl +++ b/bin/agat_convert_sp_gff2zff.pl @@ -208,7 +208,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_convert_sp_gxf2gxf.pl b/bin/agat_convert_sp_gxf2gxf.pl index 25a272aa..050961bf 100755 --- a/bin/agat_convert_sp_gxf2gxf.pl +++ b/bin/agat_convert_sp_gxf2gxf.pl @@ -112,7 +112,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_Prokka_inferNameFromAttributes.pl b/bin/agat_sp_Prokka_inferNameFromAttributes.pl index ffd02151..0edbba24 100755 --- a/bin/agat_sp_Prokka_inferNameFromAttributes.pl +++ b/bin/agat_sp_Prokka_inferNameFromAttributes.pl @@ -160,7 +160,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_add_attribute_shortest_exon_size.pl b/bin/agat_sp_add_attribute_shortest_exon_size.pl index 47358197..eac5c07e 100755 --- a/bin/agat_sp_add_attribute_shortest_exon_size.pl +++ b/bin/agat_sp_add_attribute_shortest_exon_size.pl @@ -180,7 +180,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_add_attribute_shortest_intron_size.pl b/bin/agat_sp_add_attribute_shortest_intron_size.pl index e31581e5..fb4fdbd6 100755 --- a/bin/agat_sp_add_attribute_shortest_intron_size.pl +++ b/bin/agat_sp_add_attribute_shortest_intron_size.pl @@ -189,7 +189,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_add_introns.pl b/bin/agat_sp_add_introns.pl index d65c40ba..2e1304d4 100755 --- a/bin/agat_sp_add_introns.pl +++ b/bin/agat_sp_add_introns.pl @@ -202,7 +202,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_add_start_and_stop.pl b/bin/agat_sp_add_start_and_stop.pl index d52b6c35..a70bfe26 100755 --- a/bin/agat_sp_add_start_and_stop.pl +++ b/bin/agat_sp_add_start_and_stop.pl @@ -407,7 +407,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_alignment_output_style.pl b/bin/agat_sp_alignment_output_style.pl index 1584566f..a767dfb5 100755 --- a/bin/agat_sp_alignment_output_style.pl +++ b/bin/agat_sp_alignment_output_style.pl @@ -105,7 +105,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl b/bin/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl index 632e01e0..21dc1f21 100755 --- a/bin/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl +++ b/bin/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl @@ -268,7 +268,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_compare_two_BUSCOs.pl b/bin/agat_sp_compare_two_BUSCOs.pl index a27f6c43..b477c780 100755 --- a/bin/agat_sp_compare_two_BUSCOs.pl +++ b/bin/agat_sp_compare_two_BUSCOs.pl @@ -366,7 +366,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_compare_two_annotations.pl b/bin/agat_sp_compare_two_annotations.pl index 370d5ba1..30ee0228 100755 --- a/bin/agat_sp_compare_two_annotations.pl +++ b/bin/agat_sp_compare_two_annotations.pl @@ -692,7 +692,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_complement_annotations.pl b/bin/agat_sp_complement_annotations.pl index 7b496e6e..e3b25833 100755 --- a/bin/agat_sp_complement_annotations.pl +++ b/bin/agat_sp_complement_annotations.pl @@ -191,7 +191,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_ensembl_output_style.pl b/bin/agat_sp_ensembl_output_style.pl index 063ff947..c8269abb 100755 --- a/bin/agat_sp_ensembl_output_style.pl +++ b/bin/agat_sp_ensembl_output_style.pl @@ -109,7 +109,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_extract_attributes.pl b/bin/agat_sp_extract_attributes.pl index e0236fa6..b30646f4 100755 --- a/bin/agat_sp_extract_attributes.pl +++ b/bin/agat_sp_extract_attributes.pl @@ -297,7 +297,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_extract_sequences.pl b/bin/agat_sp_extract_sequences.pl index 566780c9..dca93b8e 100755 --- a/bin/agat_sp_extract_sequences.pl +++ b/bin/agat_sp_extract_sequences.pl @@ -1054,7 +1054,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =back diff --git a/bin/agat_sp_filter_by_ORF_size.pl b/bin/agat_sp_filter_by_ORF_size.pl index 53478dd0..56e0c8be 100755 --- a/bin/agat_sp_filter_by_ORF_size.pl +++ b/bin/agat_sp_filter_by_ORF_size.pl @@ -262,7 +262,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_filter_by_locus_distance.pl b/bin/agat_sp_filter_by_locus_distance.pl index f12ae050..f4a8c65f 100755 --- a/bin/agat_sp_filter_by_locus_distance.pl +++ b/bin/agat_sp_filter_by_locus_distance.pl @@ -292,7 +292,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_filter_by_mrnaBlastValue.pl b/bin/agat_sp_filter_by_mrnaBlastValue.pl index 762c857a..baa2909c 100755 --- a/bin/agat_sp_filter_by_mrnaBlastValue.pl +++ b/bin/agat_sp_filter_by_mrnaBlastValue.pl @@ -212,7 +212,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_filter_feature_by_attribute_presence.pl b/bin/agat_sp_filter_feature_by_attribute_presence.pl index 9cdb8664..0f3c3c3f 100755 --- a/bin/agat_sp_filter_feature_by_attribute_presence.pl +++ b/bin/agat_sp_filter_feature_by_attribute_presence.pl @@ -329,7 +329,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_filter_feature_by_attribute_value.pl b/bin/agat_sp_filter_feature_by_attribute_value.pl index f03d8e00..fca55338 100755 --- a/bin/agat_sp_filter_feature_by_attribute_value.pl +++ b/bin/agat_sp_filter_feature_by_attribute_value.pl @@ -361,7 +361,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_filter_feature_from_keep_list.pl b/bin/agat_sp_filter_feature_from_keep_list.pl index 91f5f072..e4f32e4c 100755 --- a/bin/agat_sp_filter_feature_from_keep_list.pl +++ b/bin/agat_sp_filter_feature_from_keep_list.pl @@ -297,7 +297,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_filter_feature_from_kill_list.pl b/bin/agat_sp_filter_feature_from_kill_list.pl index a2c901af..dd81a410 100755 --- a/bin/agat_sp_filter_feature_from_kill_list.pl +++ b/bin/agat_sp_filter_feature_from_kill_list.pl @@ -319,7 +319,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_filter_gene_by_intron_numbers.pl b/bin/agat_sp_filter_gene_by_intron_numbers.pl index b837f027..5ca56faa 100755 --- a/bin/agat_sp_filter_gene_by_intron_numbers.pl +++ b/bin/agat_sp_filter_gene_by_intron_numbers.pl @@ -266,7 +266,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_filter_gene_by_length.pl b/bin/agat_sp_filter_gene_by_length.pl index f60cb56b..4a776284 100755 --- a/bin/agat_sp_filter_gene_by_length.pl +++ b/bin/agat_sp_filter_gene_by_length.pl @@ -290,7 +290,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_filter_incomplete_gene_coding_models.pl b/bin/agat_sp_filter_incomplete_gene_coding_models.pl index 8e48f620..0234e370 100755 --- a/bin/agat_sp_filter_incomplete_gene_coding_models.pl +++ b/bin/agat_sp_filter_incomplete_gene_coding_models.pl @@ -377,7 +377,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_filter_record_by_coordinates.pl b/bin/agat_sp_filter_record_by_coordinates.pl index 8c622c0d..edc45210 100755 --- a/bin/agat_sp_filter_record_by_coordinates.pl +++ b/bin/agat_sp_filter_record_by_coordinates.pl @@ -299,7 +299,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_fix_cds_phases.pl b/bin/agat_sp_fix_cds_phases.pl index a28f1cd3..a237d6ae 100755 --- a/bin/agat_sp_fix_cds_phases.pl +++ b/bin/agat_sp_fix_cds_phases.pl @@ -117,7 +117,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_fix_features_locations_duplicated.pl b/bin/agat_sp_fix_features_locations_duplicated.pl index 20beaedc..7421da2a 100755 --- a/bin/agat_sp_fix_features_locations_duplicated.pl +++ b/bin/agat_sp_fix_features_locations_duplicated.pl @@ -542,7 +542,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_fix_fusion.pl b/bin/agat_sp_fix_fusion.pl index 3645ef20..52277325 100755 --- a/bin/agat_sp_fix_fusion.pl +++ b/bin/agat_sp_fix_fusion.pl @@ -1435,7 +1435,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_fix_longest_ORF.pl b/bin/agat_sp_fix_longest_ORF.pl index 88bbbc04..6fddecbe 100755 --- a/bin/agat_sp_fix_longest_ORF.pl +++ b/bin/agat_sp_fix_longest_ORF.pl @@ -1268,7 +1268,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_fix_overlaping_genes.pl b/bin/agat_sp_fix_overlaping_genes.pl index 8e743897..a3726bfd 100755 --- a/bin/agat_sp_fix_overlaping_genes.pl +++ b/bin/agat_sp_fix_overlaping_genes.pl @@ -334,7 +334,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_fix_small_exon_from_extremities.pl b/bin/agat_sp_fix_small_exon_from_extremities.pl index 2da8fb19..13799c01 100755 --- a/bin/agat_sp_fix_small_exon_from_extremities.pl +++ b/bin/agat_sp_fix_small_exon_from_extremities.pl @@ -317,7 +317,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_flag_premature_stop_codons.pl b/bin/agat_sp_flag_premature_stop_codons.pl index 59bd59a5..d7e4f248 100755 --- a/bin/agat_sp_flag_premature_stop_codons.pl +++ b/bin/agat_sp_flag_premature_stop_codons.pl @@ -309,7 +309,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_flag_short_introns.pl b/bin/agat_sp_flag_short_introns.pl index 9f84aa22..e81cbebe 100755 --- a/bin/agat_sp_flag_short_introns.pl +++ b/bin/agat_sp_flag_short_introns.pl @@ -269,7 +269,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_functional_statistics.pl b/bin/agat_sp_functional_statistics.pl index 1836fb86..c6e7cc30 100755 --- a/bin/agat_sp_functional_statistics.pl +++ b/bin/agat_sp_functional_statistics.pl @@ -470,7 +470,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_keep_longest_isoform.pl b/bin/agat_sp_keep_longest_isoform.pl index e9acd12f..f826d425 100755 --- a/bin/agat_sp_keep_longest_isoform.pl +++ b/bin/agat_sp_keep_longest_isoform.pl @@ -111,7 +111,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_kraken_assess_liftover.pl b/bin/agat_sp_kraken_assess_liftover.pl index a248c038..05c42e47 100755 --- a/bin/agat_sp_kraken_assess_liftover.pl +++ b/bin/agat_sp_kraken_assess_liftover.pl @@ -776,7 +776,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_list_short_introns.pl b/bin/agat_sp_list_short_introns.pl index 8fefd9ff..4d13bcd6 100755 --- a/bin/agat_sp_list_short_introns.pl +++ b/bin/agat_sp_list_short_introns.pl @@ -205,7 +205,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_load_function_from_protein_align.pl b/bin/agat_sp_load_function_from_protein_align.pl index 605f8a85..8da4bf79 100755 --- a/bin/agat_sp_load_function_from_protein_align.pl +++ b/bin/agat_sp_load_function_from_protein_align.pl @@ -1304,7 +1304,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_manage_IDs.pl b/bin/agat_sp_manage_IDs.pl index 7e3670f3..75d7987b 100755 --- a/bin/agat_sp_manage_IDs.pl +++ b/bin/agat_sp_manage_IDs.pl @@ -445,7 +445,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_manage_UTRs.pl b/bin/agat_sp_manage_UTRs.pl index 736a5568..658ef294 100755 --- a/bin/agat_sp_manage_UTRs.pl +++ b/bin/agat_sp_manage_UTRs.pl @@ -529,7 +529,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_manage_attributes.pl b/bin/agat_sp_manage_attributes.pl index 69c7679a..7b74371f 100755 --- a/bin/agat_sp_manage_attributes.pl +++ b/bin/agat_sp_manage_attributes.pl @@ -329,7 +329,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_manage_functional_annotation.pl b/bin/agat_sp_manage_functional_annotation.pl index d3af2060..bb23ff26 100755 --- a/bin/agat_sp_manage_functional_annotation.pl +++ b/bin/agat_sp_manage_functional_annotation.pl @@ -1208,7 +1208,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_manage_introns.pl b/bin/agat_sp_manage_introns.pl index c2e6cd7f..573d45b0 100755 --- a/bin/agat_sp_manage_introns.pl +++ b/bin/agat_sp_manage_introns.pl @@ -363,7 +363,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_merge_annotations.pl b/bin/agat_sp_merge_annotations.pl index 45b79b6e..c4d99d33 100755 --- a/bin/agat_sp_merge_annotations.pl +++ b/bin/agat_sp_merge_annotations.pl @@ -119,7 +119,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sp_prokka_fix_fragmented_gene_annotations.pl b/bin/agat_sp_prokka_fix_fragmented_gene_annotations.pl index dfdcda3d..ff8cd8bd 100755 --- a/bin/agat_sp_prokka_fix_fragmented_gene_annotations.pl +++ b/bin/agat_sp_prokka_fix_fragmented_gene_annotations.pl @@ -1074,7 +1074,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_sensitivity_specificity.pl b/bin/agat_sp_sensitivity_specificity.pl index 6f65fd78..dd87c8b4 100755 --- a/bin/agat_sp_sensitivity_specificity.pl +++ b/bin/agat_sp_sensitivity_specificity.pl @@ -690,7 +690,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_separate_by_record_type.pl b/bin/agat_sp_separate_by_record_type.pl index 36ffc337..183648db 100755 --- a/bin/agat_sp_separate_by_record_type.pl +++ b/bin/agat_sp_separate_by_record_type.pl @@ -214,7 +214,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_statistics.pl b/bin/agat_sp_statistics.pl index 9849d7bb..422aa7bc 100755 --- a/bin/agat_sp_statistics.pl +++ b/bin/agat_sp_statistics.pl @@ -153,7 +153,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sp_webApollo_compliant.pl b/bin/agat_sp_webApollo_compliant.pl index 329bd28d..ff427f80 100755 --- a/bin/agat_sp_webApollo_compliant.pl +++ b/bin/agat_sp_webApollo_compliant.pl @@ -101,7 +101,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sq_add_attributes_from_tsv.pl b/bin/agat_sq_add_attributes_from_tsv.pl index fd1ebbb9..a8de5d83 100755 --- a/bin/agat_sq_add_attributes_from_tsv.pl +++ b/bin/agat_sq_add_attributes_from_tsv.pl @@ -199,7 +199,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_add_hash_tag.pl b/bin/agat_sq_add_hash_tag.pl index ed91d82b..1dfb4fdf 100755 --- a/bin/agat_sq_add_hash_tag.pl +++ b/bin/agat_sq_add_hash_tag.pl @@ -173,7 +173,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_add_locus_tag.pl b/bin/agat_sq_add_locus_tag.pl index fa52c10d..bf4fa6aa 100755 --- a/bin/agat_sq_add_locus_tag.pl +++ b/bin/agat_sq_add_locus_tag.pl @@ -217,7 +217,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_count_attributes.pl b/bin/agat_sq_count_attributes.pl index 00ac7859..527da588 100755 --- a/bin/agat_sq_count_attributes.pl +++ b/bin/agat_sq_count_attributes.pl @@ -134,7 +134,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sq_filter_feature_from_fasta.pl b/bin/agat_sq_filter_feature_from_fasta.pl index c827a6c8..e5f87fd1 100755 --- a/bin/agat_sq_filter_feature_from_fasta.pl +++ b/bin/agat_sq_filter_feature_from_fasta.pl @@ -134,7 +134,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_list_attributes.pl b/bin/agat_sq_list_attributes.pl index a5b0e64f..8b807377 100755 --- a/bin/agat_sq_list_attributes.pl +++ b/bin/agat_sq_list_attributes.pl @@ -217,7 +217,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sq_manage_IDs.pl b/bin/agat_sq_manage_IDs.pl index 482c6a0d..6594e159 100755 --- a/bin/agat_sq_manage_IDs.pl +++ b/bin/agat_sq_manage_IDs.pl @@ -157,7 +157,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_manage_attributes.pl b/bin/agat_sq_manage_attributes.pl index f6f6bc41..da4dab47 100755 --- a/bin/agat_sq_manage_attributes.pl +++ b/bin/agat_sq_manage_attributes.pl @@ -377,7 +377,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sq_mask.pl b/bin/agat_sq_mask.pl index c6da77d7..b5bbb3c4 100755 --- a/bin/agat_sq_mask.pl +++ b/bin/agat_sq_mask.pl @@ -172,7 +172,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<-h> or B<--help> diff --git a/bin/agat_sq_remove_redundant_entries.pl b/bin/agat_sq_remove_redundant_entries.pl index d0d6f43b..b817e040 100755 --- a/bin/agat_sq_remove_redundant_entries.pl +++ b/bin/agat_sq_remove_redundant_entries.pl @@ -138,7 +138,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_rename_seqid.pl b/bin/agat_sq_rename_seqid.pl index 380a8410..247f2178 100755 --- a/bin/agat_sq_rename_seqid.pl +++ b/bin/agat_sq_rename_seqid.pl @@ -145,7 +145,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_repeats_analyzer.pl b/bin/agat_sq_repeats_analyzer.pl index 86b98786..f33bc7b5 100755 --- a/bin/agat_sq_repeats_analyzer.pl +++ b/bin/agat_sq_repeats_analyzer.pl @@ -199,7 +199,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_reverse_complement.pl b/bin/agat_sq_reverse_complement.pl index 99a2bd39..924d507d 100755 --- a/bin/agat_sq_reverse_complement.pl +++ b/bin/agat_sq_reverse_complement.pl @@ -181,7 +181,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_rfam_analyzer.pl b/bin/agat_sq_rfam_analyzer.pl index afccf583..114d69d1 100755 --- a/bin/agat_sq_rfam_analyzer.pl +++ b/bin/agat_sq_rfam_analyzer.pl @@ -206,7 +206,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_split.pl b/bin/agat_sq_split.pl index 24725016..492b5db1 100755 --- a/bin/agat_sq_split.pl +++ b/bin/agat_sq_split.pl @@ -146,7 +146,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/bin/agat_sq_stat_basic.pl b/bin/agat_sq_stat_basic.pl index eb940cbe..6244154f 100755 --- a/bin/agat_sq_stat_basic.pl +++ b/bin/agat_sq_stat_basic.pl @@ -206,7 +206,7 @@ =head1 OPTIONS String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". -The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently). +The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). =item B<--help> or B<-h> diff --git a/docs/tools/agat_convert_bed2gff.md b/docs/tools/agat_convert_bed2gff.md index 02923870..bf93fa20 100644 --- a/docs/tools/agat_convert_bed2gff.md +++ b/docs/tools/agat_convert_bed2gff.md @@ -50,6 +50,12 @@ agat_convert_bed2gff.pl -h Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_convert_embl2gff.md b/docs/tools/agat_convert_embl2gff.md index 5f1f2c40..584f8b32 100644 --- a/docs/tools/agat_convert_embl2gff.md +++ b/docs/tools/agat_convert_embl2gff.md @@ -40,6 +40,12 @@ agat_converter_embl2gff.pl --embl infile.embl [ -o outfile ] Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_convert_genscan2gff.md b/docs/tools/agat_convert_genscan2gff.md index 5c9b9db3..c6df47fd 100644 --- a/docs/tools/agat_convert_genscan2gff.md +++ b/docs/tools/agat_convert_genscan2gff.md @@ -57,6 +57,12 @@ agat_convert_genscan2gff.pl -h Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_convert_mfannot2gff.md b/docs/tools/agat_convert_mfannot2gff.md index c6a5d20c..a3c211f4 100644 --- a/docs/tools/agat_convert_mfannot2gff.md +++ b/docs/tools/agat_convert_mfannot2gff.md @@ -28,6 +28,12 @@ modified by jacques dainat 2017-11 the gff output file +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_convert_minimap2_bam2gff.md b/docs/tools/agat_convert_minimap2_bam2gff.md index 544081b8..6bf437d1 100644 --- a/docs/tools/agat_convert_minimap2_bam2gff.md +++ b/docs/tools/agat_convert_minimap2_bam2gff.md @@ -36,6 +36,12 @@ if ( !GetOptions( 'i|input=s' => \\$opt\_in, Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_convert_sp_gff2bed.md b/docs/tools/agat_convert_sp_gff2bed.md index 2be64c0e..bbe9e20e 100644 --- a/docs/tools/agat_convert_sp_gff2bed.md +++ b/docs/tools/agat_convert_sp_gff2bed.md @@ -46,6 +46,12 @@ agat_convert_sp_gff2bed.pl --help File where will be written the result. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_convert_sp_gff2gtf.md b/docs/tools/agat_convert_sp_gff2gtf.md index 1bad1585..7947acf1 100644 --- a/docs/tools/agat_convert_sp_gff2gtf.md +++ b/docs/tools/agat_convert_sp_gff2gtf.md @@ -53,6 +53,12 @@ agat_convert_sp_gff2gtf -h Output GTF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_convert_sp_gff2tsv.md b/docs/tools/agat_convert_sp_gff2tsv.md index e60079a0..a44c76ce 100644 --- a/docs/tools/agat_convert_sp_gff2tsv.md +++ b/docs/tools/agat_convert_sp_gff2tsv.md @@ -23,6 +23,12 @@ agat_convert_sp_gff2tsv.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_convert_sp_gff2zff.md b/docs/tools/agat_convert_sp_gff2zff.md index 80964350..0f8b0931 100644 --- a/docs/tools/agat_convert_sp_gff2zff.md +++ b/docs/tools/agat_convert_sp_gff2zff.md @@ -29,6 +29,12 @@ agat_convert_sp_gff2zff.pl --help File prefix where will be written the results (e.g. outfile.ann and outfile.dna). If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_convert_sp_gxf2gxf.md b/docs/tools/agat_convert_sp_gxf2gxf.md index b3595b1e..885baa23 100644 --- a/docs/tools/agat_convert_sp_gxf2gxf.md +++ b/docs/tools/agat_convert_sp_gxf2gxf.md @@ -33,6 +33,12 @@ agat_convert_sp_gxf2gxf.pl --help String - Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Boolean - Display this helpful text. diff --git a/docs/tools/agat_sp_Prokka_inferNameFromAttributes.md b/docs/tools/agat_sp_Prokka_inferNameFromAttributes.md index 56d1cf8e..804cb5f1 100644 --- a/docs/tools/agat_sp_Prokka_inferNameFromAttributes.md +++ b/docs/tools/agat_sp_Prokka_inferNameFromAttributes.md @@ -28,6 +28,12 @@ agat_sp_Prokka_inferNameFromAttributes.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_add_attribute_shortest_exon_size.md b/docs/tools/agat_sp_add_attribute_shortest_exon_size.md index 0fa62101..06bf344d 100644 --- a/docs/tools/agat_sp_add_attribute_shortest_exon_size.md +++ b/docs/tools/agat_sp_add_attribute_shortest_exon_size.md @@ -25,6 +25,12 @@ agat_sp_add_attribute_shortest_exon_size.pl --help BOLEAN: Verbose for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_add_attribute_shortest_intron_size.md b/docs/tools/agat_sp_add_attribute_shortest_intron_size.md index 3945a784..878c977b 100644 --- a/docs/tools/agat_sp_add_attribute_shortest_intron_size.md +++ b/docs/tools/agat_sp_add_attribute_shortest_intron_size.md @@ -25,6 +25,12 @@ agat_sp_add_attribute_shortest_intron_size.pl --help BOLEAN: Verbose for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_add_introns.md b/docs/tools/agat_sp_add_introns.md index c0040ea3..41dbbb9d 100644 --- a/docs/tools/agat_sp_add_introns.md +++ b/docs/tools/agat_sp_add_introns.md @@ -21,6 +21,12 @@ agat_sp_add_introns.pl --help Output GFF3 file. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_add_start_and_stop.md b/docs/tools/agat_sp_add_start_and_stop.md index a805daf4..4908e7db 100644 --- a/docs/tools/agat_sp_add_start_and_stop.md +++ b/docs/tools/agat_sp_add_start_and_stop.md @@ -35,6 +35,12 @@ agat_sp_add_start_and_stop.pl.pl --help Verbose for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_alignment_output_style.md b/docs/tools/agat_sp_alignment_output_style.md index 7a2bca90..f3f6d554 100644 --- a/docs/tools/agat_sp_alignment_output_style.md +++ b/docs/tools/agat_sp_alignment_output_style.md @@ -34,6 +34,12 @@ agat_sp_alignment_output_style.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_clipN_seqExtremities_and_fixCoordinates.md b/docs/tools/agat_sp_clipN_seqExtremities_and_fixCoordinates.md index 2be458f0..c808a6a2 100644 --- a/docs/tools/agat_sp_clipN_seqExtremities_and_fixCoordinates.md +++ b/docs/tools/agat_sp_clipN_seqExtremities_and_fixCoordinates.md @@ -32,6 +32,12 @@ agat_sp_clipN_seqExtremities_and_fixCoordinates.pl --help Output fixed GFF file. If no output file is specified, the output will be written to STDOUT +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_compare_two_BUSCOs.md b/docs/tools/agat_sp_compare_two_BUSCOs.md index f34d18a7..f54bc04f 100644 --- a/docs/tools/agat_sp_compare_two_BUSCOs.md +++ b/docs/tools/agat_sp_compare_two_BUSCOs.md @@ -42,6 +42,12 @@ agat_sp_compare_two_BUSCOs.pl --help STRING: Output folder. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_compare_two_annotations.md b/docs/tools/agat_sp_compare_two_annotations.md index 8b1d1a36..4a8cb028 100644 --- a/docs/tools/agat_sp_compare_two_annotations.md +++ b/docs/tools/agat_sp_compare_two_annotations.md @@ -40,6 +40,12 @@ agat_sp_compare_two_annotations.pl --help Verbose option, make it easier to follow what is going on for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_complement_annotations.md b/docs/tools/agat_sp_complement_annotations.md index fefe8541..5d2ccd6f 100644 --- a/docs/tools/agat_sp_complement_annotations.md +++ b/docs/tools/agat_sp_complement_annotations.md @@ -37,6 +37,12 @@ agat_sp_complement_annotations.pl --help Output gff3 containing the reference annotation with all the non-overlapping newly added genes from addfiles.gff. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_ensembl_output_style.md b/docs/tools/agat_sp_ensembl_output_style.md index 7ace8cf4..1868a4c6 100644 --- a/docs/tools/agat_sp_ensembl_output_style.md +++ b/docs/tools/agat_sp_ensembl_output_style.md @@ -33,6 +33,12 @@ agat_sp_ensembl_output_style.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_extract_attributes.md b/docs/tools/agat_sp_extract_attributes.md index 11f96dcf..33b0f6a2 100644 --- a/docs/tools/agat_sp_extract_attributes.md +++ b/docs/tools/agat_sp_extract_attributes.md @@ -46,6 +46,12 @@ agat_sp_extract_attributes.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_extract_sequences.md b/docs/tools/agat_sp_extract_sequences.md index 3fe7c528..45956e84 100644 --- a/docs/tools/agat_sp_extract_sequences.md +++ b/docs/tools/agat_sp_extract_sequences.md @@ -135,6 +135,12 @@ agat_sp_extract_sequences.pl --help String - Input GTF/GFF file. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Boolean - Display this helpful text. diff --git a/docs/tools/agat_sp_filter_by_ORF_size.md b/docs/tools/agat_sp_filter_by_ORF_size.md index d7880267..3ca23ff9 100644 --- a/docs/tools/agat_sp_filter_by_ORF_size.md +++ b/docs/tools/agat_sp_filter_by_ORF_size.md @@ -36,6 +36,12 @@ By default it will be ">" Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_filter_by_locus_distance.md b/docs/tools/agat_sp_filter_by_locus_distance.md index 3aa7ba8f..d64cc9d2 100644 --- a/docs/tools/agat_sp_filter_by_locus_distance.md +++ b/docs/tools/agat_sp_filter_by_locus_distance.md @@ -39,6 +39,12 @@ agat_sp_filter_by_locus_distance.pl --help Verbose option, make it easier to follow what is going on for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_filter_by_mrnaBlastValue.md b/docs/tools/agat_sp_filter_by_mrnaBlastValue.md index 3ab85dcf..a4a8df92 100644 --- a/docs/tools/agat_sp_filter_by_mrnaBlastValue.md +++ b/docs/tools/agat_sp_filter_by_mrnaBlastValue.md @@ -29,6 +29,12 @@ agat_sp_filter_by_mrnaBlastValue.pl --help The name of the output file. By default the output is the standard output. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_filter_feature_by_attribute_presence.md b/docs/tools/agat_sp_filter_feature_by_attribute_presence.md index 562060f5..15c73389 100644 --- a/docs/tools/agat_sp_filter_feature_by_attribute_presence.md +++ b/docs/tools/agat_sp_filter_feature_by_attribute_presence.md @@ -43,6 +43,12 @@ agat_sp_select_feature_by_attribute_presence.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_filter_feature_by_attribute_value.md b/docs/tools/agat_sp_filter_feature_by_attribute_value.md index a41ae15e..1c63bcb6 100644 --- a/docs/tools/agat_sp_filter_feature_by_attribute_value.md +++ b/docs/tools/agat_sp_filter_feature_by_attribute_value.md @@ -50,6 +50,12 @@ Test to apply (> < = >= <=). default value "=". If you us one of these two chara Verbose option for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_filter_feature_from_keep_list.md b/docs/tools/agat_sp_filter_feature_from_keep_list.md index 4fef7e9c..9070acbc 100644 --- a/docs/tools/agat_sp_filter_feature_from_keep_list.md +++ b/docs/tools/agat_sp_filter_feature_from_keep_list.md @@ -47,6 +47,12 @@ agat_sp_filter_feature_from_keep_list.pl --help Verbose option for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_filter_feature_from_kill_list.md b/docs/tools/agat_sp_filter_feature_from_kill_list.md index eadabdb7..794b4126 100644 --- a/docs/tools/agat_sp_filter_feature_from_kill_list.md +++ b/docs/tools/agat_sp_filter_feature_from_kill_list.md @@ -47,6 +47,12 @@ agat_sp_filter_feature_from_kill_list.pl --help Verbose option for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_filter_gene_by_intron_numbers.md b/docs/tools/agat_sp_filter_gene_by_intron_numbers.md index 51889011..c4eee777 100644 --- a/docs/tools/agat_sp_filter_gene_by_intron_numbers.md +++ b/docs/tools/agat_sp_filter_gene_by_intron_numbers.md @@ -42,6 +42,12 @@ please do not forget to quote your parameter like that "<=". Else your terminal Verbose option for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_filter_gene_by_length.md b/docs/tools/agat_sp_filter_gene_by_length.md index 50191ecf..4adc1fe6 100644 --- a/docs/tools/agat_sp_filter_gene_by_length.md +++ b/docs/tools/agat_sp_filter_gene_by_length.md @@ -47,6 +47,12 @@ agat_sp_filter_gene_by_length.pl --help Verbose option for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_filter_incomplete_gene_coding_models.md b/docs/tools/agat_sp_filter_incomplete_gene_coding_models.md index 8d95de5f..d82899cd 100644 --- a/docs/tools/agat_sp_filter_incomplete_gene_coding_models.md +++ b/docs/tools/agat_sp_filter_incomplete_gene_coding_models.md @@ -50,6 +50,12 @@ agat_sp_filter_incomplete_gene_coding_models.pl --help Verbose option, make it easier to follow what is going on for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_filter_record_by_coordinates.md b/docs/tools/agat_sp_filter_record_by_coordinates.md index 100afd4a..688ec134 100644 --- a/docs/tools/agat_sp_filter_record_by_coordinates.md +++ b/docs/tools/agat_sp_filter_record_by_coordinates.md @@ -24,7 +24,7 @@ agat_sp_filter_record_by_coordinates.pl --help Input GTF/GFF file -- **-c**, **--coordinates**, **--tsv**, **-r** or **--ranges** +- **--coordinates**, **--tsv**, **-r** or **--ranges** String - tsv file containing the coordinates. Coordinates must be one per line. @@ -46,6 +46,12 @@ agat_sp_filter_record_by_coordinates.pl --help Verbosity. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_fix_cds_phases.md b/docs/tools/agat_sp_fix_cds_phases.md index 4413f378..e0a5236a 100644 --- a/docs/tools/agat_sp_fix_cds_phases.md +++ b/docs/tools/agat_sp_fix_cds_phases.md @@ -30,6 +30,12 @@ agat_sp_fix_cds_frame.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_fix_features_locations_duplicated.md b/docs/tools/agat_sp_fix_features_locations_duplicated.md index 7d127f65..e9729683 100644 --- a/docs/tools/agat_sp_fix_features_locations_duplicated.md +++ b/docs/tools/agat_sp_fix_features_locations_duplicated.md @@ -46,6 +46,12 @@ agat_sp_fix_features_locations_duplicated.pl --help Output file. If none given, will be display in standard output. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_fix_fusion.md b/docs/tools/agat_sp_fix_fusion.md index 32e105dc..2628dec4 100644 --- a/docs/tools/agat_sp_fix_fusion.md +++ b/docs/tools/agat_sp_fix_fusion.md @@ -47,6 +47,12 @@ agat_sp_fix_fusion.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_fix_longest_ORF.md b/docs/tools/agat_sp_fix_longest_ORF.md index 76858078..78e06a28 100644 --- a/docs/tools/agat_sp_fix_longest_ORF.md +++ b/docs/tools/agat_sp_fix_longest_ORF.md @@ -70,6 +70,12 @@ agat_sp_fix_longest_ORF.pl --help verbose mode. Default off. -v 1 minimum verbosity, -v 3 maximum verbosity +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_fix_overlaping_genes.md b/docs/tools/agat_sp_fix_overlaping_genes.md index 402e72b7..0973262a 100644 --- a/docs/tools/agat_sp_fix_overlaping_genes.md +++ b/docs/tools/agat_sp_fix_overlaping_genes.md @@ -32,6 +32,12 @@ agat_sp_fix_overlaping_genes.pl --help BOLEAN: Add verbosity. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_fix_small_exon_from_extremities.md b/docs/tools/agat_sp_fix_small_exon_from_extremities.md index d62f3d71..bbd9b91f 100644 --- a/docs/tools/agat_sp_fix_small_exon_from_extremities.md +++ b/docs/tools/agat_sp_fix_small_exon_from_extremities.md @@ -42,6 +42,12 @@ agat_fix_small_exon_from_extremities.pl --help Verbose option, make it easier to follow what is going on for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_flag_premature_stop_codons.md b/docs/tools/agat_sp_flag_premature_stop_codons.md index 4b528764..e947cfa9 100644 --- a/docs/tools/agat_sp_flag_premature_stop_codons.md +++ b/docs/tools/agat_sp_flag_premature_stop_codons.md @@ -32,6 +32,12 @@ agat_sp_flag_premature_stop_codons.pl --help Output gff3 file where the result will be printed. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_flag_short_introns.md b/docs/tools/agat_sp_flag_short_introns.md index bfb739f4..c38c8183 100644 --- a/docs/tools/agat_sp_flag_short_introns.md +++ b/docs/tools/agat_sp_flag_short_introns.md @@ -33,6 +33,12 @@ agat_sp_flag_short_introns.pl --help Bolean. Verbose for debugging purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_functional_statistics.md b/docs/tools/agat_sp_functional_statistics.md index 521244bf..15a9864b 100644 --- a/docs/tools/agat_sp_functional_statistics.md +++ b/docs/tools/agat_sp_functional_statistics.md @@ -26,6 +26,12 @@ agat_sp_functional_statistics.pl --help Folder where will be written the results. \[Default output_functional_statistics\] +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_keep_longest_isoform.md b/docs/tools/agat_sp_keep_longest_isoform.md index b7273692..a35c93aa 100644 --- a/docs/tools/agat_sp_keep_longest_isoform.md +++ b/docs/tools/agat_sp_keep_longest_isoform.md @@ -24,6 +24,12 @@ agat_sp_keep_longest_isoform.pl --help File where will be written the result. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_kraken_assess_liftover.md b/docs/tools/agat_sp_kraken_assess_liftover.md index 72859683..2896978f 100644 --- a/docs/tools/agat_sp_kraken_assess_liftover.md +++ b/docs/tools/agat_sp_kraken_assess_liftover.md @@ -41,6 +41,12 @@ agat_sp_kraken_assess_lift_coverage --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_list_short_introns.md b/docs/tools/agat_sp_list_short_introns.md index a5106fbc..06a308b3 100644 --- a/docs/tools/agat_sp_list_short_introns.md +++ b/docs/tools/agat_sp_list_short_introns.md @@ -27,6 +27,12 @@ agat_sp_list_short_introns.pl --help Output gff3 file where the gene incriminated will be write. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_load_function_from_protein_align.md b/docs/tools/agat_sp_load_function_from_protein_align.md index 9c5af853..c03479f8 100644 --- a/docs/tools/agat_sp_load_function_from_protein_align.md +++ b/docs/tools/agat_sp_load_function_from_protein_align.md @@ -79,6 +79,12 @@ agat_sp_load_function_from_protein_align.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_manage_IDs.md b/docs/tools/agat_sp_manage_IDs.md index 68ab2b7b..4ee24152 100644 --- a/docs/tools/agat_sp_manage_IDs.md +++ b/docs/tools/agat_sp_manage_IDs.md @@ -82,6 +82,12 @@ agat_sp_manage_IDs.pl --help String - Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Boolean - Display this helpful text. diff --git a/docs/tools/agat_sp_manage_UTRs.md b/docs/tools/agat_sp_manage_UTRs.md index 621eb2fa..1b0cfd29 100644 --- a/docs/tools/agat_sp_manage_UTRs.md +++ b/docs/tools/agat_sp_manage_UTRs.md @@ -44,6 +44,12 @@ agat_sp_manage_UTRs.pl --help Output gff3 file where the gene incriminated will be write. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_manage_attributes.md b/docs/tools/agat_sp_manage_attributes.md index b48610b9..54a048bf 100644 --- a/docs/tools/agat_sp_manage_attributes.md +++ b/docs/tools/agat_sp_manage_attributes.md @@ -57,6 +57,12 @@ agat_sp_manage_attributes.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_manage_functional_annotation.md b/docs/tools/agat_sp_manage_functional_annotation.md index 4719faa2..c9ff70e6 100644 --- a/docs/tools/agat_sp_manage_functional_annotation.md +++ b/docs/tools/agat_sp_manage_functional_annotation.md @@ -129,6 +129,12 @@ agat_sp_manage_functional_annotation.pl --help Boolean - Verbose, for debug purpose. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Boolean - Display this helpful text. diff --git a/docs/tools/agat_sp_manage_introns.md b/docs/tools/agat_sp_manage_introns.md index 0339a0df..051346f9 100644 --- a/docs/tools/agat_sp_manage_introns.md +++ b/docs/tools/agat_sp_manage_introns.md @@ -35,6 +35,12 @@ agat_sp_manage_introns.pl --help Output gff3 file where the gene incriminated will be write. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_merge_annotations.md b/docs/tools/agat_sp_merge_annotations.md index e44fd69a..c526a063 100644 --- a/docs/tools/agat_sp_merge_annotations.md +++ b/docs/tools/agat_sp_merge_annotations.md @@ -22,6 +22,12 @@ agat_sp_merge_annotations.pl --help Output gff3 file where the gene incriminated will be write. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sp_prokka_fix_fragmented_gene_annotations.md b/docs/tools/agat_sp_prokka_fix_fragmented_gene_annotations.md index 80803c1a..04cbd2d4 100644 --- a/docs/tools/agat_sp_prokka_fix_fragmented_gene_annotations.md +++ b/docs/tools/agat_sp_prokka_fix_fragmented_gene_annotations.md @@ -83,6 +83,12 @@ agat_sp_prokka_fragmented_gene_annotations.pl --help verbose mode. Default off. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_sensitivity_specificity.md b/docs/tools/agat_sp_sensitivity_specificity.md index 38eefee3..9b83a4d3 100644 --- a/docs/tools/agat_sp_sensitivity_specificity.md +++ b/docs/tools/agat_sp_sensitivity_specificity.md @@ -43,6 +43,12 @@ agat_sp_sensitivity_specificity.pl --help Verbose option for debug purposes. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_separate_by_record_type.md b/docs/tools/agat_sp_separate_by_record_type.md index c05e4365..dc542528 100644 --- a/docs/tools/agat_sp_separate_by_record_type.md +++ b/docs/tools/agat_sp_separate_by_record_type.md @@ -27,6 +27,12 @@ agat_sp_separate_by_record_type.pl --help Output folder. If no output folder provided, the default name will be <split\_result>. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_split_by_level2_feature.md b/docs/tools/agat_sp_split_by_level2_feature.md index 9c0e2079..25c144e9 100644 --- a/docs/tools/agat_sp_split_by_level2_feature.md +++ b/docs/tools/agat_sp_split_by_level2_feature.md @@ -22,6 +22,12 @@ agat_sp_split_by_level2_feature.pl --help Output folder. If no output folder provided, the default name will be <split\_result>. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_statistics.md b/docs/tools/agat_sp_statistics.md index ff48f067..28550cb5 100644 --- a/docs/tools/agat_sp_statistics.md +++ b/docs/tools/agat_sp_statistics.md @@ -39,6 +39,12 @@ agat_sp_statistics.pl --help File where will be written the result. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_to_tabulated.md b/docs/tools/agat_sp_to_tabulated.md index d6bac822..a5eaa0b3 100644 --- a/docs/tools/agat_sp_to_tabulated.md +++ b/docs/tools/agat_sp_to_tabulated.md @@ -35,6 +35,12 @@ agat_sp_to_tabulated.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sp_webApollo_compliant.md b/docs/tools/agat_sp_webApollo_compliant.md index 4ad2b3b9..0a63ca97 100644 --- a/docs/tools/agat_sp_webApollo_compliant.md +++ b/docs/tools/agat_sp_webApollo_compliant.md @@ -24,6 +24,12 @@ agat_sp_webApollo_compliant.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sq_add_attributes_from_tsv.md b/docs/tools/agat_sq_add_attributes_from_tsv.md index 08ae3dda..70fd7d3a 100644 --- a/docs/tools/agat_sq_add_attributes_from_tsv.md +++ b/docs/tools/agat_sq_add_attributes_from_tsv.md @@ -61,6 +61,12 @@ agat_sq_add_attributes_from_tsv.pl --help STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sq_add_hash_tag.md b/docs/tools/agat_sq_add_hash_tag.md index 3c071037..9f76ba24 100644 --- a/docs/tools/agat_sq_add_hash_tag.md +++ b/docs/tools/agat_sq_add_hash_tag.md @@ -28,6 +28,12 @@ agat_sq_add_hash_tag.pl --help STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sq_add_locus_tag.md b/docs/tools/agat_sq_add_locus_tag.md index a3a642a6..261db8c1 100644 --- a/docs/tools/agat_sq_add_locus_tag.md +++ b/docs/tools/agat_sq_add_locus_tag.md @@ -45,6 +45,12 @@ agat_sq_add_locus_tag.pl --help To remove verbosity. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sq_count_attributes.md b/docs/tools/agat_sq_count_attributes.md index cc93ce86..5685369a 100644 --- a/docs/tools/agat_sq_count_attributes.md +++ b/docs/tools/agat_sq_count_attributes.md @@ -27,6 +27,12 @@ agat_sq_count_attributes.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sq_filter_feature_from_fasta.md b/docs/tools/agat_sq_filter_feature_from_fasta.md index cef5bc8d..7222fc0d 100644 --- a/docs/tools/agat_sq_filter_feature_from_fasta.md +++ b/docs/tools/agat_sq_filter_feature_from_fasta.md @@ -31,6 +31,12 @@ agat_sq_filter_feature_from_fasta.pl --help STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sq_list_attributes.md b/docs/tools/agat_sq_list_attributes.md index 8760a6e8..43fd372f 100644 --- a/docs/tools/agat_sq_list_attributes.md +++ b/docs/tools/agat_sq_list_attributes.md @@ -32,6 +32,12 @@ agat_sq_list_attributes.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sq_manage_ID.md b/docs/tools/agat_sq_manage_ID.md index faa181ef..adbe73ed 100644 --- a/docs/tools/agat_sq_manage_ID.md +++ b/docs/tools/agat_sq_manage_ID.md @@ -26,6 +26,12 @@ agat_sq_manage_ID.pl --help STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sq_manage_IDs.md b/docs/tools/agat_sq_manage_IDs.md index faa181ef..adbe73ed 100644 --- a/docs/tools/agat_sq_manage_IDs.md +++ b/docs/tools/agat_sq_manage_IDs.md @@ -26,6 +26,12 @@ agat_sq_manage_ID.pl --help STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sq_manage_attributes.md b/docs/tools/agat_sq_manage_attributes.md index 133bd30a..18b7c2fa 100644 --- a/docs/tools/agat_sq_manage_attributes.md +++ b/docs/tools/agat_sq_manage_attributes.md @@ -67,6 +67,12 @@ agat_sq_manage_attributes.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sq_mask.md b/docs/tools/agat_sq_mask.md index e976f0be..b6b03fbe 100644 --- a/docs/tools/agat_sq_mask.md +++ b/docs/tools/agat_sq_mask.md @@ -36,6 +36,12 @@ agat_sq_mask.pl --help Output GFF file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **-h** or **--help** Display this helpful text. diff --git a/docs/tools/agat_sq_remove_redundant_entries.md b/docs/tools/agat_sq_remove_redundant_entries.md index 27e7e0ce..0b2b95b6 100644 --- a/docs/tools/agat_sq_remove_redundant_entries.md +++ b/docs/tools/agat_sq_remove_redundant_entries.md @@ -23,6 +23,12 @@ agat_sq_remove_redundant_entries.pl --help STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sq_repeats_analyzer.md b/docs/tools/agat_sq_repeats_analyzer.md index 5b5d81f6..d3eacf73 100644 --- a/docs/tools/agat_sq_repeats_analyzer.md +++ b/docs/tools/agat_sq_repeats_analyzer.md @@ -27,6 +27,12 @@ agat_sq_repeats_analyzer.pl --help STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sq_reverse_complement.md b/docs/tools/agat_sq_reverse_complement.md index eb9a7be2..013df142 100644 --- a/docs/tools/agat_sq_reverse_complement.md +++ b/docs/tools/agat_sq_reverse_complement.md @@ -30,6 +30,12 @@ agat_sq_reverse_complement.pl --help STRING: Output file. If no output file is specified, the output will be written to STDOUT. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** BOOLEAN: Display this helpful text. diff --git a/docs/tools/agat_sq_rfam_analyzer.md b/docs/tools/agat_sq_rfam_analyzer.md index 173d1b4f..ac2a4e02 100644 --- a/docs/tools/agat_sq_rfam_analyzer.md +++ b/docs/tools/agat_sq_rfam_analyzer.md @@ -30,6 +30,12 @@ agat_sq_rfam_analyzer.pl --help STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sq_split.md b/docs/tools/agat_sq_split.md index 4f78e47a..e6b0e94c 100644 --- a/docs/tools/agat_sq_split.md +++ b/docs/tools/agat_sq_split.md @@ -27,6 +27,12 @@ The top feature of the feature group. By default "gene". STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text. diff --git a/docs/tools/agat_sq_stat_basic.md b/docs/tools/agat_sq_stat_basic.md index 90542cf0..30b5a5af 100644 --- a/docs/tools/agat_sq_stat_basic.md +++ b/docs/tools/agat_sq_stat_basic.md @@ -34,6 +34,12 @@ agat_sq_stat_basic.pl --help STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format. +- **-c** or **--config** + + String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". + The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + - **--help** or **-h** Display this helpful text.