diff agat.xml @ 5:e7449b2c14bf draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 28a6a1644ff8ffd8c3a47ccaaad0cb2da2aa87e3

--- 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[