Mercurial > repos > bgruening > agat

changeset 5:e7449b2c14bf draft

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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 -------------------------------------
Binary file test-data/test01_plot1.pdf has changed
--- 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:
 
 ----------------------------------------------------------------------------------------------