# HG changeset patch
# User yating-l
# Date 1529948198 14400
# Node ID bd4d459469598428203f7d2952de1296367c1573
# Parent  75d9357a0a53d1eef05199e2f25417ef49e0dcf3
planemo upload commit 58057cff13206fae66c938464c052f416047c1b3-dirty

diff -r 75d9357a0a53 -r bd4d45946959 rename_tracks.xml
--- a/rename_tracks.xml	Mon Jun 25 13:12:47 2018 -0400
+++ b/rename_tracks.xml	Mon Jun 25 13:36:38 2018 -0400
@@ -8,7 +8,7 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        python $__tool_directory__/rename_tracks.py "${input}" "${mapping}" $format_select.format "${output}"
+        python $__tool_directory__/rename_tracks.py "${format_select.input}" "${mapping}" $format_select.format "${output}"
         #if $format_select.format == "bigwig"
             "${format_select.reference}"
         #end if
@@ -16,7 +16,6 @@
 
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="gff3,gtf,bed,bam" label="Custom track file" />
         <conditional name="format_select">
             <param name="format" type="select" label="Select the format of your custom track file">
                 <option value="bed">BED</option>
@@ -25,12 +24,24 @@
                 <option value="bam">BAM</option>
                 <option value="bigwig">BigWig</option>
             </param>
+            <when value="bed">
+                <param name="input" type="data" format="bed" label="Custom track file" />
+            </when>
+            <when value="gff3">
+                <param name="input" type="data" format="gff3" label="Custom track file" />
+            </when>
+            <when value="gtf">
+                <param name="input" type="data" format="gtf" label="Custom track file" />
+            </when>
+            <when value="bam">
+                <param name="input" type="data" format="bam" label="Custom track file" />
+            </when>
             <when value="bigwig">
+                <param name="input" type="data" format="bigwig" label="Custom track file" />
                 <param name="reference" type="data" format="fasta" label="Provide the renamed the reference file from 'renamed the scaffolds' tool" />
             </when>
         </conditional>
         <param name="mapping" type="data" format="csv" label="Provide the name mapping file from 'renamed the scaffolds' tool"/>
-
     </inputs>
     <outputs>
         <data name="output" format_source="input" label="${tool.name} on ${on_string}: renamed_track" />