diff agat.xml @ 6:d6ede73082da draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit df456b8d319fd0a629829fba0f5819117b7936d3

--- a/agat.xml	Wed Aug 07 20:54:27 2024 +0000
+++ b/agat.xml	Fri Oct 18 13:34:42 2024 +0000
@@ -143,12 +143,19 @@
                 --config '$agat_configfile'
                 --output ./output &&
             cat ./output > '${annotation}'
+        #else if $tool.selector == 'fix_overlapping_genes'
+            @input_annotation_single@
+            agat_sp_fix_overlaping_genes.pl
+                --gff '$input_annotation'
+                --config '$agat_configfile'
+                --output ./output &&
+            cat ./output > '${annotation}'
         #end if
         ]]>
     </command>
         <configfiles>
         <configfile name="agat_configfile"><![CDATA[
-#if $tool.selector in ['fix','merge_annotations','complement','splice_sites','filter_feature_fasta','keep_longest_isoform']
+#if $tool.selector in ['fix','merge_annotations','complement','splice_sites','filter_feature_fasta','keep_longest_isoform', 'fix_overlapping_genes']
 ---
 output_format: $tool.output_format.selector
 #if $tool.output_format.selector == "GFF"
@@ -202,6 +209,7 @@
                 <option value="merge_annotations">Merge annotations (agat_sp_merge_annotations.pl)</option>
                 <option value="functional_annotation">Functional annotation (agat_sp_manage_functional_annotation.pl)</option>
                 <option value="keep_longest_isoform">Keep longest isoform (agat_sp_keep_longest_isoform.pl)</option>
+                <option value="fix_overlapping_genes">Fix Overlapping Genes (agat_sp_fix_overlaping_genes.pl)</option>
             </param>
             <when value="annotation_statistics">
                 <expand macro="ANNOTATION_INPUT"/>
@@ -333,6 +341,10 @@
                 <expand macro="ANNOTATION_INPUT" format="gff,gff3,gff3.gz"/>
                 <expand macro="AGAT_CONFIG"/>
             </when>
+            <when value="fix_overlapping_genes">
+                <expand macro="ANNOTATION_INPUT" format="gff,gff3,gff3.gz"/>
+                <expand macro="AGAT_CONFIG"/>
+            </when>
         </conditional>
     </inputs>
     <outputs>
@@ -343,7 +355,7 @@
             <filter>tool['selector'] == 'convert_GFF2GTF'</filter>
         </data>
         <data name="annotation" format="gff3" label="${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>
+            <filter>tool['selector'] in ['fix','merge_annotations','complement','filter_feature_fasta','splice_sites','bam2gff','keep_longest_isoform', 'fix_overlapping_genes']</filter>
             <change_format>
                 <when input="output_format.selector" value="GTF" format="gtf" />
             </change_format>
@@ -566,6 +578,14 @@
             </conditional>
             <output name="annotation" file="test15.gff" ftype="gff3"/>
         </test>
+        <!-- Test 16: Fix overlapping genes -->
+        <test expect_num_outputs="1">
+            <conditional name="tool">
+                <param name="selector" value="fix_overlapping_genes"/>
+                <param name="gff" value="test16_input.gff"/>
+            </conditional>
+            <output name="annotation" file="test16.gff" ftype="gff3"/>
+        </test>
     </tests>
     <help><![CDATA[