diff --git a/bin/agat_convert_bed2gff.pl b/bin/agat_convert_bed2gff.pl index b7a8790..4149cb4 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 1dc76cc..720d33f 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 6d671d7..6bcfdfa 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 70e2607..e6ebc7b 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 881f7df..44ca42e 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 fb7a621..f189be6 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 a7fb126..b64cd2c 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 8fad53d..723ffd9 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 d1c7ce0..bbb9580 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 25a272a..050961b 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 ffd0215..0edbba2 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 4735819..eac5c07 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 e31581e..fb4fdbd 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 d65c40b..2e1304d 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 d52b6c3..a70bfe2 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 1584566..a767dfb 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 632e01e..21dc1f2 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 a27f6c4..b477c78 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 370d5ba..30ee022 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 7b496e6..e3b2583 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 063ff94..c8269ab 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 e0236fa..b30646f 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 566780c..dca93b8 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 53478dd..56e0c8b 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 f12ae05..f4a8c65 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 762c857..baa2909 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 9cdb866..0f3c3c3 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 f03d8e0..fca5533 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 91f5f07..e4f32e4 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 a2c901a..dd81a41 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 b837f02..5ca56fa 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 f60cb56..4a77628 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 8e48f62..0234e37 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 8c622c0..edc4521 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 a28f1cd..a237d6a 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 20beaed..7421da2 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 3645ef2..5227732 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 88bbbc0..6fddecb 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 8e74389..a3726bf 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 2da8fb1..13799c0 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 59bd59a..d7e4f24 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 9f84aa2..e81cbeb 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 1836fb8..c6e7cc3 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 e9acd12..f826d42 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 a248c03..05c42e4 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 8fefd9f..4d13bcd 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 605f8a8..8da4bf7 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 7e3670f..75d7987 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 736a556..658ef29 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 69c7679..7b74371 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 d3af206..bb23ff2 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 c2e6cd7..573d45b 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 45b79b6..c4d99d3 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 dfdcda3..ff8cd8b 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 6f65fd7..dd87c8b 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 36ffc33..183648d 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 9849d7b..422aa7b 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 329bd28..ff427f8 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 fd1ebbb..a8de5d8 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 ed91d82..1dfb4fd 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 fa52c10..bf4fa6a 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 00ac785..527da58 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 c827a6c..e5f87fd 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 a5b0e64..8b80737 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 482c6a0..6594e15 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 f6f6bc4..da4dab4 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 c6da77d..b5bbb3c 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 d0d6f43..b817e04 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 380a841..247f217 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 86b9878..f33bc7b 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 99a2bd3..924d507 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 afccf58..114d69d 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 2472501..492b5db 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 eb940cb..6244154 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 0292387..bf93fa2 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 5f1f2c4..584f8b3 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 5c9b9db..c6df47f 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 c6a5d20..a3c211f 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 544081b..6bf437d 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 2be64c0..bbe9e20 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 1bad158..7947acf 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 e60079a..a44c76c 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 8096435..0f8b093 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 b3595b1..885baa2 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 56d1cf8..804cb5f 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 0fa6210..06bf344 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 3945a78..878c977 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 c0040ea..41dbbb9 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 a805daf..4908e7d 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 7a2bca9..f3f6d55 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 2be458f..c808a6a 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 f34d18a..f54bc04 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 8b1d1a3..4a8cb02 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 fefe854..5d2ccd6 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 7ace8cf..1868a4c 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 11f96dc..33b0f6a 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 3fe7c52..45956e8 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 d788026..3ca23ff 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 3aa7ba8..d64cc9d 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 3ab85dc..a4a8df9 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 562060f..15c7338 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 a41ae15..1c63bcb 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 4fef7e9..9070acb 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 eadabdb..794b412 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 5188901..c4eee77 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 50191ec..4adc1fe 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 8d95de5..d82899c 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 100afd4..688ec13 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 4413f37..e0a5236 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 7d127f6..e972968 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 32e105d..2628dec 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 7685807..78e06a2 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 402e72b..0973262 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 d62f3d7..bbd9b91 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 4b52876..e947cfa 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 bfb739f..c38c818 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 521244b..15a9864 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 b727369..a35c93a 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 7285968..2896978 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 a5106fb..06a308b 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 9c5af85..c03479f 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 68ab2b7..4ee2415 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 621eb2f..1b0cfd2 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 b48610b..54a048b 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 4719faa..c9ff70e 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 0339a0d..051346f 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 e44fd69..c526a06 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 80803c1..04cbd2d 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 38eefee..9b83a4d 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 c05e436..dc54252 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 9c0e207..25c144e 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 ff48f06..28550cb 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 d6bac82..a5eaa0b 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 4ad2b3b..0a63ca9 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 08ae3dd..70fd7d3 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 3c07103..9f76ba2 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 a3a642a..261db8c 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 cc93ce8..5685369 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 cef5bc8..7222fc0 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 8760a6e..43fd372 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 faa181e..adbe73e 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 faa181e..adbe73e 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 133bd30..18b7c2f 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 e976f0b..b6b03fb 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 27e7e0c..0b2b95b 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 5b5d81f..d3eacf7 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 eb9a7be..013df14 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 173d1b4..ac2a4e0 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 4f78e47..e6b0e94 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 90542cf..30b5a5a 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.