--- a/fromgtfTobed12.xml	Fri Nov 04 15:37:12 2022 +0000
+++ b/fromgtfTobed12.xml	Fri Nov 03 14:13:51 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="fromgtfTobed12" name="fromgtftobed12" version="0.11.1+galaxy0">
+<tool id="fromgtfTobed12" name="fromgtftobed12" version="0.11.1+galaxy1">
   <description> Convert a gtf to a bed12.</description>
   <requirements>
     <requirement type="package" version="0.11.1">gffutils</requirement>
@@ -14,7 +14,9 @@
   <command>
 <![CDATA[
         python3 $__tool_directory__/fromgtfTobed12.py
-        $useGene
+        #if str($preferedName) != "":
+          --preferedName $preferedName
+        #end if
         $mergeTranscripts
         $ucscformat
         --output $output
@@ -23,12 +25,12 @@
   </command>
   <inputs>
     <param name="input" multiple="false" type="data" format="gtf" label="Select the gtf to convert."/>
-    <param argument="--useGene" type="boolean" checked="False" truevalue="--useGene" falsevalue="" label="Uses the gene name instead of the transcript name."/>
     <param name="mergeTranscripts" type="select" label="Do you want to merge all transcripts of a gene in a single line?">
       <option value="" selected="true">No</option>
       <option value="--mergeTranscripts">Yes</option>
       <option value="--mergeTranscriptsAndOverlappingExons">Yes and merge overlapping exons</option>
     </param>
+    <param argument="--preferedName" type="text" value="" label="Use a specific name for the 4th column" help="By default the 4th column will be transcript_name or gene_name if you merge transcripts. If you prefer 'gene_id', for example, then set this option." />
     <param argument="--ucscformat" type="boolean" checked="True" truevalue="--ucscformat" falsevalue="" label="If you want that all chromosome names begin with 'chr'."/>
   </inputs>
   
@@ -45,20 +47,24 @@
     <test>
       <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
       <param name="ucscformat" value="--ucscformat"/>
-      <param name="useGene" value="--useGene"/>
+      <param name="preferedName" value="gene_name"/>
       <output name="output" file="testWithGenes.bed"/>
     </test>
     <test>
       <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
+      <param name="ucscformat" value="--ucscformat"/>
+      <param name="preferedName" value="gene_id"/>
+      <output name="output" file="testWithGeneIds.bed"/>
+    </test>
+    <test>
+      <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
       <param name="mergeTranscripts" value="--mergeTranscripts"/>
-      <param name="useGene" value="--useGene"/>
       <param name="ucscformat" value=""/>
       <output name="output" file="testMergeNotUCSC.bed"/>
     </test>
     <test>
       <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
       <param name="mergeTranscripts" value="--mergeTranscriptsAndOverlappingExons"/>
-      <param name="useGene" value="--useGene"/>
       <param name="ucscformat" value=""/>
       <output name="output" file="testMergeExons.bed"/>
     </test>