# HG changeset patch
# User iuc
# Date 1592326910 14400
# Node ID 679d93c99757caa1b78bbfd773e27b3ac3f1d5ed
# Parent  6dc45faebc1d41afdd5acffea0336c5ef90c0857
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"

diff -r 6dc45faebc1d -r 679d93c99757 cuff_macros.xml
--- a/cuff_macros.xml	Sun Feb 19 12:09:41 2017 -0500
+++ b/cuff_macros.xml	Tue Jun 16 13:01:50 2020 -0400
@@ -66,20 +66,26 @@
   </token>
   <xml name="cufflinks_gtf_inputs">
     <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
-    <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)">
-      <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" />
-    </repeat>
   </xml>
+  <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[
+            ## Inputs.
+            #for $i, $input_file in enumerate($inputs):
+                ln -s '${input_file}' input_$i &&
+            #end for
+  ]]></token>
   <token name="@CUFFLINKS_GTF_INPUTS@">
             ## Inputs.
-            #for $input_file in $inputs:
-                '${input_file}'
-            #end for
-            #for $additional_input in $additional_inputs:
-                #for $input_file in $additional_input.additional_inputs:
-                    '${input_file}'
-                #end for
+            #for $i, $input_file in enumerate($inputs):
+                'input_$i'
             #end for
   </token>
   <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
+
+  <xml name="citations">
+    <citations>
+        <citation type="doi">10.1038/nbt.1621</citation>
+        <yield/>
+    </citations>
+  </xml>
+
 </macros>
diff -r 6dc45faebc1d -r 679d93c99757 cuffquant_wrapper.xml
--- a/cuffquant_wrapper.xml	Sun Feb 19 12:09:41 2017 -0500
+++ b/cuffquant_wrapper.xml	Tue Jun 16 13:01:50 2020 -0400
@@ -5,7 +5,7 @@
       <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <version_command>cuffquant 2>&amp;1 | head -n 1</version_command>
+    <version_command><![CDATA[cuffquant 2>&1 | head -n 1]]></version_command>
     <command detect_errors="aggressive"><![CDATA[
         cuffquant
             --no-update-check
@@ -211,7 +211,5 @@
   --mask-file (gff3/gtf)         Ignore all alignment within transcripts in this file
   --max-bundle-frags             Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.
     </help>
-    <citations>
-        <citation type="doi">10.1038/nbt.1621</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>