Mercurial > repos > bgruening > agat
changeset 5:e7449b2c14bf draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 28a6a1644ff8ffd8c3a47ccaaad0cb2da2aa87e3
author | bgruening |
---|---|
date | Wed, 07 Aug 2024 20:54:27 +0000 |
parents | abba05ead5d7 |
children | d6ede73082da |
files | agat.xml macros.xml test-data/annotation_fixed.gff test-data/functional_annot/report.txt test-data/test01_plot1.pdf test-data/test03.txt |
diffstat | 6 files changed, 27 insertions(+), 26 deletions(-) [+] |
line wrap: on
line diff
--- a/agat.xml Fri Jul 26 15:21:48 2024 +0000 +++ b/agat.xml Wed Aug 07 20:54:27 2024 +0000 @@ -40,7 +40,7 @@ --gff1 '$input1' --gff2 '$input2' --output ./temp_output && - cat ./temp_output > '${stats_output}' + cat ./temp_output/report.txt > '${stats_output}' #else if $tool.selector == 'extract' @input_annotation_single@ @input_reference@ @@ -182,6 +182,7 @@ check_all_level2_locations: true check_all_level1_locations: true check_identical_isoforms: true +clean_attributes_from_template: false #end if ]]></configfile> </configfiles> @@ -335,13 +336,13 @@ </conditional> </inputs> <outputs> - <data name="annotation_gff" format="gff" label="${tool.name} on ${on_string}: annotation file (GFF)"> + <data name="annotation_gff" format="gff3" label="${tool.name} on ${on_string}: annotation file (GFF)"> <filter>tool['selector'] == 'convert_GTF2GFF'</filter> </data> <data name="annotation_gtf" format="gtf" label="${tool.name} on ${on_string}: annotation file (GTF)"> <filter>tool['selector'] == 'convert_GFF2GTF'</filter> </data> - <data name="annotation" format="gff" label="${tool.name} on ${on_string}: annotation file"> + <data name="annotation" format="gff3" label="${tool.name} on ${on_string}: annotation file"> <filter>tool['selector'] in ['fix','merge_annotations','complement','filter_feature_fasta','splice_sites','bam2gff','keep_longest_isoform']</filter> <change_format> <when input="output_format.selector" value="GTF" format="gtf" /> @@ -438,13 +439,13 @@ <param name="version" value="3"/> </conditional> </conditional> - <output name="annotation_gff" file="test04.gff" ftype="gff"/> + <output name="annotation_gff" file="test04.gff" ftype="gff3"/> </test> <!-- Test 05: Convert GFF2GTF --> <test expect_num_outputs="1"> <conditional name="tool"> <param name="selector" value="convert_GFF2GTF"/> - <param name="gff" value="test04.gff" ftype="gff"/> + <param name="gff" value="test04.gff" ftype="gff3"/> <param name="gtf_version" value="2"/> </conditional> <output name="annotation_gtf" file="test05.gtf" ftype="gtf"/> @@ -455,7 +456,7 @@ <param name="selector" value="convert_GTF2GFF"/> <param name="gff" value="annotation_small.gtf" ftype="gtf"/> </conditional> - <output name="annotation_gff" file="test06.gff" ftype="gff"/> + <output name="annotation_gff" file="test06.gff" ftype="gff3"/> </test> <!-- Test 07: Filter feature FASTA --> <test expect_num_outputs="1"> @@ -467,15 +468,15 @@ <param name="history_item" value="genome.fasta.gz"/> </conditional> </conditional> - <output name="annotation" file="test07.gff" ftype="gff"/> + <output name="annotation" file="test07.gff" ftype="gff3"/> </test> <!-- Test 08: Fix annotation file --> <test expect_num_outputs="1"> <conditional name="tool"> <param name="selector" value="fix"/> - <param name="gff" value="annotation_broken.gff" ftype="gff"/> + <param name="gff" value="annotation_broken.gff" ftype="gff3"/> </conditional> - <output name="annotation_gff" file="annotation_fixed.gff" ftype="gff"/> + <output name="annotation_gff" file="annotation_fixed.gff" ftype="gff3"/> <assert_stdout> <has_text text="2 exons created that were missing" /> </assert_stdout> @@ -503,15 +504,15 @@ <param name="selector" value="gff"/> <param name="version" value="3"/> </conditional> - <output name="annotation_gff" file="test10.gff" ftype="gff"/> + <output name="annotation_gff" file="test10.gff" ftype="gff3"/> </test> <!-- Test 11: Test compressed files --> <test expect_num_outputs="1"> <conditional name="tool"> <param name="selector" value="fix"/> - <param name="gff" value="annotation_broken.gff.gz" ftype="gff"/> + <param name="gff" value="annotation_broken.gff.gz" ftype="gff3"/> </conditional> - <output name="annotation_gff" file="annotation_fixed.gff" ftype="gff"/> + <output name="annotation_gff" file="annotation_fixed.gff" ftype="gff3"/> <assert_stdout> <has_text text="2 exons created that were missing" /> </assert_stdout> @@ -535,15 +536,15 @@ <test expect_num_outputs="1"> <conditional name="tool"> <param name="selector" value="splice_sites"/> - <param name="gff" value="test04.gff" ftype="gff"/> + <param name="gff" value="test04.gff" ftype="gff3"/> </conditional> - <output name="annotation" file="test13.gff" ftype="gff"/> + <output name="annotation" file="test13.gff" ftype="gff3"/> </test> <!-- Test 14: Functional annotation --> <test expect_num_outputs="7"> <conditional name="tool"> <param name="selector" value="functional_annotation"/> - <param name="gff" value="annotation_fixed.gff" ftype="gff"/> + <param name="gff" value="annotation_fixed.gff" ftype="gff3"/> <param name="input_interpro" value="interpro_input.tabular"/> <conditional name="blast_adv"> <param name="options" value="no"/> @@ -563,7 +564,7 @@ <param name="selector" value="keep_longest_isoform"/> <param name="gff" value="annotation_dup.gff"/> </conditional> - <output name="annotation" file="test15.gff" ftype="gff"/> + <output name="annotation" file="test15.gff" ftype="gff3"/> </test> </tests> <help><![CDATA[
--- a/macros.xml Fri Jul 26 15:21:48 2024 +0000 +++ b/macros.xml Wed Aug 07 20:54:27 2024 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">1.2.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">1.4.0</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">agat</requirement>
--- a/test-data/annotation_fixed.gff Fri Jul 26 15:21:48 2024 +0000 +++ b/test-data/annotation_fixed.gff Wed Aug 07 20:54:27 2024 +0000 @@ -14,11 +14,11 @@ NZ_CP027599.1 Protein Homology CDS 1052 2152 . + 0 ID=cds-WP_000673464.1;Parent=gene-C7A06_RS00010;Dbxref=Genbank:WP_000673464.1;Name=WP_000673464.1;Ontology_term=GO:0006260,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;gene_id=nbis-gene-2;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006177590.1;locus_tag=C7A06_RS00010;product=DNA polymerase III subunit beta;protein_id=WP_000673464.1;transcript_id=gene-C7A06_RS00010;transl_table=11 NZ_CP027599.1 RefSeq gene 2152 3225 . + . ID=nbis-gene-3;Name=recF;gbkey=Gene;gene=recF;gene_biotype=protein_coding;gene_id=nbis-gene-3;locus_tag=C7A06_RS00015 NZ_CP027599.1 RefSeq transcript 2152 3225 . + . ID=gene-C7A06_RS00015;Parent=nbis-gene-3;Name=recF;gbkey=Gene;gene=recF;gene_biotype=protein_coding;gene_id=nbis-gene-3;locus_tag=C7A06_RS00015;original_biotype=mrna;transcript_id=gene-C7A06_RS00015 -NZ_CP027599.1 Protein Homology exon 2152 3225 . + . ID=nbis-exon-1;Parent=gene-C7A06_RS00015;Dbxref=Genbank:WP_000060112.1;Name=WP_000060112.1;Ontology_term=GO:0006281,GO:0003697,GO:0005524;gbkey=CDS;gene=recF;gene_id=nbis-gene-3;go_function=single-stranded DNA binding|0003697||IEA,ATP binding|0005524||IEA;go_process=DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121479.1;locus_tag=C7A06_RS00015;product=DNA replication/repair protein RecF;protein_id=WP_000060112.1;transcript_id=gene-C7A06_RS00015;transl_table=11 +NZ_CP027599.1 AGAT exon 2152 3225 . + . ID=nbis-exon-1;Parent=gene-C7A06_RS00015;Dbxref=Genbank:WP_000060112.1;Name=WP_000060112.1;Ontology_term=GO:0006281,GO:0003697,GO:0005524;gbkey=CDS;gene=recF;gene_id=nbis-gene-3;go_function=single-stranded DNA binding|0003697||IEA,ATP binding|0005524||IEA;go_process=DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121479.1;locus_tag=C7A06_RS00015;product=DNA replication/repair protein RecF;protein_id=WP_000060112.1;transcript_id=gene-C7A06_RS00015;transl_table=11 NZ_CP027599.1 Protein Homology CDS 2152 3225 . + 0 ID=cds-WP_000060112.1;Parent=gene-C7A06_RS00015;Dbxref=Genbank:WP_000060112.1;Name=WP_000060112.1;Ontology_term=GO:0006281,GO:0003697,GO:0005524;gbkey=CDS;gene=recF;gene_id=nbis-gene-3;go_function=single-stranded DNA binding|0003697||IEA,ATP binding|0005524||IEA;go_process=DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121479.1;locus_tag=C7A06_RS00015;product=DNA replication/repair protein RecF;protein_id=WP_000060112.1;transcript_id=gene-C7A06_RS00015;transl_table=11 NZ_CP027599.1 RefSeq gene 3254 5668 . + . ID=nbis-gene-4;Name=gyrB;gbkey=Gene;gene=gyrB;gene_biotype=protein_coding;gene_id=nbis-gene-4;locus_tag=C7A06_RS00020 -NZ_CP027599.1 RefSeq mRNA 3254 5668 . + . ID=gene-C7A06_RS00020;Parent=nbis-gene-4;Name=gyrB;gbkey=Gene;gene=gyrB;gene_biotype=protein_coding;gene_id=nbis-gene-4;locus_tag=C7A06_RS00020 -NZ_CP027599.1 Protein Homology exon 3254 5668 . + . ID=nbis-exon-3;Parent=gene-C7A06_RS00020;Dbxref=Genbank:WP_000072067.1;Name=WP_000072067.1;Ontology_term=GO:0006265,GO:0003918,GO:0009330;gbkey=CDS;gene=gyrB;gene_id=nbis-gene-4;go_component=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) complex|0009330||IEA;go_function=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) activity|0003918||IEA;go_process=DNA topological change|0006265||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121480.1;locus_tag=C7A06_RS00020;product=DNA topoisomerase (ATP-hydrolyzing) subunit B;protein_id=WP_000072067.1;transcript_id=gene-C7A06_RS00020;transl_table=11 +NZ_CP027599.1 AGAT mRNA 3254 5668 . + . ID=gene-C7A06_RS00020;Parent=nbis-gene-4;Dbxref=Genbank:WP_000072067.1;Name=WP_000072067.1;Ontology_term=GO:0006265,GO:0003918,GO:0009330;gbkey=CDS;gene=gyrB;gene_id=nbis-gene-4;go_component=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) complex|0009330||IEA;go_function=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) activity|0003918||IEA;go_process=DNA topological change|0006265||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121480.1;locus_tag=C7A06_RS00020;product=DNA topoisomerase (ATP-hydrolyzing) subunit B;protein_id=WP_000072067.1;transcript_id=gene-C7A06_RS00020;transl_table=11 +NZ_CP027599.1 AGAT exon 3254 5668 . + . ID=nbis-exon-3;Parent=gene-C7A06_RS00020;Dbxref=Genbank:WP_000072067.1;Name=WP_000072067.1;Ontology_term=GO:0006265,GO:0003918,GO:0009330;gbkey=CDS;gene=gyrB;gene_id=nbis-gene-4;go_component=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) complex|0009330||IEA;go_function=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) activity|0003918||IEA;go_process=DNA topological change|0006265||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121480.1;locus_tag=C7A06_RS00020;product=DNA topoisomerase (ATP-hydrolyzing) subunit B;protein_id=WP_000072067.1;transcript_id=gene-C7A06_RS00020;transl_table=11 NZ_CP027599.1 Protein Homology CDS 3254 5668 . + 0 ID=cds-WP_000072067.1;Parent=gene-C7A06_RS00020;Dbxref=Genbank:WP_000072067.1;Name=WP_000072067.1;Ontology_term=GO:0006265,GO:0003918,GO:0009330;gbkey=CDS;gene=gyrB;gene_id=nbis-gene-4;go_component=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) complex|0009330||IEA;go_function=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) activity|0003918||IEA;go_process=DNA topological change|0006265||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_005121480.1;locus_tag=C7A06_RS00020;product=DNA topoisomerase (ATP-hydrolyzing) subunit B;protein_id=WP_000072067.1;transcript_id=gene-C7A06_RS00020;transl_table=11 NZ_CP027599.1 RefSeq gene 5908 6306 . + . ID=nbis-gene-5;Name=yidB;gbkey=Gene;gene=yidB;gene_biotype=protein_coding;gene_id=nbis-gene-5;locus_tag=C7A06_RS00025 NZ_CP027599.1 RefSeq transcript 5908 6306 . + . ID=gene-C7A06_RS00025;Parent=nbis-gene-5;Name=yidB;gbkey=Gene;gene=yidB;gene_biotype=protein_coding;gene_id=nbis-gene-5;locus_tag=C7A06_RS00025;original_biotype=mrna;transcript_id=gene-C7A06_RS00025 @@ -27,7 +27,7 @@ NZ_CP027599.1 RefSeq gene 6421 7233 . + . ID=nbis-gene-6;Name=yidA;gbkey=Gene;gene=yidA;gene_biotype=protein_coding;gene_id=nbis-gene-6;locus_tag=C7A06_RS00030 NZ_CP027599.1 RefSeq transcript 6421 7233 . + . ID=gene-C7A06_RS00030;Parent=nbis-gene-6;Name=yidA;gbkey=Gene;gene=yidA;gene_biotype=protein_coding;gene_id=nbis-gene-6;locus_tag=C7A06_RS00030;original_biotype=mrna;transcript_id=gene-C7A06_RS00030 NZ_CP027599.1 Protein Homology exon 6421 7233 . + . ID=nbis-exon-6;Parent=gene-C7A06_RS00030;Dbxref=Genbank:WP_000985541.1;Name=WP_000985541.1;Ontology_term=GO:0016787;gbkey=CDS;gene=yidA;gene_id=nbis-gene-6;go_function=hydrolase activity|0016787||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418152.1;locus_tag=C7A06_RS00030;product=sugar-phosphatase;protein_id=WP_000985541.1;transcript_id=gene-C7A06_RS00030;transl_table=11 -NZ_CP027599.1 RefSeq gene 7279 7935 . - . ID=nbis-gene-7;Name=C7A06_RS00035;gbkey=Gene;gene_biotype=protein_coding;gene_id=nbis-gene-7;locus_tag=C7A06_RS00035;original_biotype=mrna;transcript_id=gene-C7A06_RS00035 +NZ_CP027599.1 AGAT gene 7279 7935 . - . ID=nbis-gene-7;Name=C7A06_RS00035;gbkey=Gene;gene_biotype=protein_coding;gene_id=nbis-gene-7;locus_tag=C7A06_RS00035;original_biotype=mrna;transcript_id=gene-C7A06_RS00035 NZ_CP027599.1 RefSeq transcript 7279 7935 . - . ID=gene-C7A06_RS00035;Parent=nbis-gene-7;Name=C7A06_RS00035;gbkey=Gene;gene_biotype=protein_coding;gene_id=nbis-gene-7;locus_tag=C7A06_RS00035;original_biotype=mrna;transcript_id=gene-C7A06_RS00035 NZ_CP027599.1 Protein Homology exon 7279 7935 . - . ID=nbis-exon-7;Parent=gene-C7A06_RS00035;Dbxref=Genbank:WP_000772931.1;Name=WP_000772931.1;gbkey=CDS;gene_id=nbis-gene-7;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709504.1;locus_tag=C7A06_RS00035;product=hypothetical protein;protein_id=WP_000772931.1;transcript_id=gene-C7A06_RS00035;transl_table=11 NZ_CP027599.1 Protein Homology CDS 7279 7935 . - 0 ID=cds-WP_000772931.1;Parent=gene-C7A06_RS00035;Dbxref=Genbank:WP_000772931.1;Name=WP_000772931.1;gbkey=CDS;gene_id=nbis-gene-7;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709504.1;locus_tag=C7A06_RS00035;product=hypothetical protein;protein_id=WP_000772931.1;transcript_id=gene-C7A06_RS00035;transl_table=11 @@ -36,7 +36,7 @@ NZ_CP027599.1 Protein Homology exon 8213 8902 . + . ID=nbis-exon-8;Parent=gene-C7A06_RS00040;Dbxref=Genbank:WP_000174305.1;Name=WP_000174305.1;gbkey=CDS;gene=dgoR;gene_id=nbis-gene-8;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709505.1;locus_tag=C7A06_RS00040;product=D-galactonate utilization transcriptional regulator DgoR;protein_id=WP_000174305.1;transcript_id=gene-C7A06_RS00040;transl_table=11 NZ_CP027599.1 Protein Homology CDS 8213 8902 . + 0 ID=cds-WP_000174305.1;Parent=gene-C7A06_RS00040;Dbxref=Genbank:WP_000174305.1;Name=WP_000174305.1;gbkey=CDS;gene=dgoR;gene_id=nbis-gene-8;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709505.1;locus_tag=C7A06_RS00040;product=D-galactonate utilization transcriptional regulator DgoR;protein_id=WP_000174305.1;transcript_id=gene-C7A06_RS00040;transl_table=11 NZ_CP027599.1 RefSeq gene 8899 9777 . + . ID=nbis-gene-9;Name=dgoK;gbkey=Gene;gene=dgoK;gene_biotype=protein_coding;gene_id=nbis-gene-9;locus_tag=C7A06_RS00045 -NZ_CP027599.1 RefSeq mRNA 8899 9777 . + . ID=gene-C7A06_RS00045;Parent=nbis-gene-9;Name=dgoK;gbkey=Gene;gene=dgoK;gene_biotype=protein_coding;gene_id=nbis-gene-9;locus_tag=C7A06_RS00045 +NZ_CP027599.1 AGAT mRNA 8899 9777 . + . ID=gene-C7A06_RS00045;Parent=nbis-gene-9;Dbxref=Genbank:WP_000127112.1;Name=WP_000127112.1;gbkey=CDS;gene=dgoK;gene_id=nbis-gene-9;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709506.1;locus_tag=C7A06_RS00045;product=2-dehydro-3-deoxygalactonokinase;protein_id=WP_000127112.1;transcript_id=gene-C7A06_RS00045;transl_table=11 NZ_CP027599.1 Protein Homology exon 8899 9777 . + . ID=nbis-exon-9;Parent=gene-C7A06_RS00045;Dbxref=Genbank:WP_000127112.1;Name=WP_000127112.1;gbkey=CDS;gene=dgoK;gene_id=nbis-gene-9;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709506.1;locus_tag=C7A06_RS00045;product=2-dehydro-3-deoxygalactonokinase;protein_id=WP_000127112.1;transcript_id=gene-C7A06_RS00045;transl_table=11 NZ_CP027599.1 Protein Homology CDS 8899 9777 . + 0 ID=cds-WP_000127112.1;Parent=gene-C7A06_RS00045;Dbxref=Genbank:WP_000127112.1;Name=WP_000127112.1;gbkey=CDS;gene=dgoK;gene_id=nbis-gene-9;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709506.1;locus_tag=C7A06_RS00045;product=2-dehydro-3-deoxygalactonokinase;protein_id=WP_000127112.1;transcript_id=gene-C7A06_RS00045;transl_table=11 NZ_CP027599.1 RefSeq gene 9761 10378 . + . ID=nbis-gene-10;Name=dgoA;gbkey=Gene;gene=dgoA;gene_biotype=protein_coding;gene_id=nbis-gene-10;locus_tag=C7A06_RS00050
--- a/test-data/functional_annot/report.txt Fri Jul 26 15:21:48 2024 +0000 +++ b/test-data/functional_annot/report.txt Wed Aug 07 20:54:27 2024 +0000 @@ -1,5 +1,5 @@ -02/15/2024 -usage: /home/rlibouba/miniconda3/envs/__agat@1.2.0/bin/agat_sp_manage_functional_annotation.pl --gff annotation.gff -i /tmp/tmpvotn3s2b/files/d/a/b/dataset_dab3424c-9f01-4319-a841-302674d17b7c.dat -pe 5 -o galaxy_functional_annot +08/07/2024 +usage: /usr/local/bin/agat_sp_manage_functional_annotation.pl --gff annotation.gff3 --interpro /tmp/tmpfrax2fi0/files/1/a/8/dataset_1a8bf643-33d2-43bd-b647-4dc301ad8c40.dat -pe 5 -o galaxy_functional_annot -------------------------------------------------------------------------------- ------------------------------------- mrna -------------------------------------
--- a/test-data/test03.txt Fri Jul 26 15:21:48 2024 +0000 +++ b/test-data/test03.txt Wed Aug 07 20:54:27 2024 +0000 @@ -1,4 +1,4 @@ -usage: /home/rlibouba/miniconda3/envs/__agat@1.2.0/bin/agat_sp_compare_two_annotations.pl --gff1 annotation1.gtf --gff2 annotation2.gtf --output ./temp_output +usage: /usr/local/bin/agat_sp_compare_two_annotations.pl --gff1 annotation1.gtf --gff2 annotation2.gtf --output ./temp_output Results of number of genes from file1 that overlap genes from file2: ----------------------------------------------------------------------------------------------