update

docs/index.rst

@@ -14,15 +14,89 @@ Contents
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
+   :caption: General:
 
    the_format.md
    why_this_tool.md
    agat_for_you.md
-   tools/tools.rst
    topological-sorting-of-gff-features.md
    troubleshooting.md
 
+   :maxdepth: 1
+   :caption: List of tools:
+   tools/agat_convert_bed2gff.md
+   tools/agat_convert_embl2gff.md
+   tools/agat_convert_genscan2gff.md
+   tools/agat_convert_mfannot2gff.md
+   tools/agat_convert_minimap2_bam2gff.md
+   tools/agat_convert_sp_gff2bed.md
+   tools/agat_convert_sp_gff2gtf.md
+   tools/agat_convert_sp_gff2tsv.md
+   tools/agat_convert_sp_gff2zff.md
+   tools/agat_convert_sp_gxf2gxf.md
+   tools/agat_sp_Prokka_inferNameFromAttributes.md
+   tools/agat_sp_add_introns.md
+   tools/agat_sp_add_start_and_stop.md
+   tools/agat_sp_alignment_output_style.md
+   tools/agat_sp_clipN_seqExtremities_and_fixCoordinates.md
+   tools/agat_sp_compare_two_BUSCOs.md
+   tools/agat_sp_compare_two_annotations.md
+   tools/agat_sp_complement_annotations.md
+   tools/agat_sp_ensembl_output_style.md
+   tools/agat_sp_extract_attributes.md
+   tools/agat_sp_extract_sequences.md
+   tools/agat_sp_filter_by_ORF_size.md
+   tools/agat_sp_filter_by_locus_distance.md
+   tools/agat_sp_filter_by_mrnaBlastValue.md
+   tools/agat_sp_filter_feature_by_attribute_presence.md
+   tools/agat_sp_filter_feature_by_attribute_value.md
+   tools/agat_sp_filter_feature_from_keep_list.md
+   tools/agat_sp_filter_feature_from_kill_list.md
+   tools/agat_sp_filter_gene_by_intron_numbers.md
+   tools/agat_sp_filter_gene_by_length.md
+   tools/agat_sp_filter_incomplete_gene_coding_models.md
+   tools/agat_sp_filter_record_by_coordinates.md
+   tools/agat_sp_fix_cds_phases.md
+   tools/agat_sp_fix_features_locations_duplicated.md
+   tools/agat_sp_fix_fusion.md
+   tools/agat_sp_fix_longest_ORF.md
+   tools/agat_sp_fix_overlaping_genes.md
+   tools/agat_sp_fix_small_exon_from_extremities.md
+   tools/agat_sp_flag_premature_stop_codons.md
+   tools/agat_sp_flag_short_introns.md
+   tools/agat_sp_functional_statistics.md
+   tools/agat_sp_gxf_to_gff3.md
+   tools/agat_sp_keep_longest_isoform.md
+   tools/agat_sp_kraken_assess_liftover.md
+   tools/agat_sp_list_short_introns.md
+   tools/agat_sp_load_function_from_protein_align.md
+   tools/agat_sp_manage_IDs.md
+   tools/agat_sp_manage_UTRs.md
+   tools/agat_sp_manage_attributes.md
+   tools/agat_sp_manage_functional_annotation.md
+   tools/agat_sp_manage_introns.md
+   tools/agat_sp_merge_annotations.md
+   tools/agat_sp_prokka_fix_fragmented_gene_annotations.md
+   tools/agat_sp_sensitivity_specificity.md
+   tools/agat_sp_separate_by_record_type.md
+   tools/agat_sp_split_by_level2_feature.md
+   tools/agat_sp_statistics.md
+   tools/agat_sp_to_tabulated.md
+   tools/agat_sp_webApollo_compliant.md
+   tools/agat_sq_add_attributes_from_tsv.md
+   tools/agat_sq_add_hash_tag.md
+   tools/agat_sq_add_locus_tag.md
+   tools/agat_sq_keep_annotation_from_fastaSeq.md
+   tools/agat_sq_list_attributes.md
+   tools/agat_sq_manage_ID.md
+   tools/agat_sq_manage_IDs.md
+   tools/agat_sq_manage_attributes.md
+   tools/agat_sq_mask.md
+   tools/agat_sq_remove_redundant_entries.md
+   tools/agat_sq_repeats_analyzer.md
+   tools/agat_sq_rfam_analyzer.md
+   tools/agat_sq_split.md
+   tools/agat_sq_stat_basic.md
 
 Indices and tables
 ==================