diff cuffcompare_wrapper.xml @ 2:a5674ddf2ad7 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f

--- a/cuffcompare_wrapper.xml	Tue Oct 13 12:37:24 2015 -0400
+++ b/cuffcompare_wrapper.xml	Tue Feb 07 18:37:50 2017 -0500
@@ -1,16 +1,16 @@
 <tool id="cuffcompare" name="Cuffcompare" version="2.2.1.0">
     <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <version_command>cuffcompare 2>&amp;1 | head -n 1</version_command>
-    <command interpreter="python">
-        cuffcompare_wrapper.py 
+    <command>
+        python '$__tool_directory__/cuffcompare_wrapper.py'
             ## Use annotation reference?
             #if $annotation.use_ref_annotation == "Yes":
-                -r $annotation.reference_annotation
+                -r '$annotation.reference_annotation'
                 #if $annotation.ignore_nonoverlapping_reference:
                     -R
                 #end if
@@ -24,9 +24,9 @@
             #if $seq_data.use_seq_data == "Yes":
             -s
                 #if $seq_data.seq_source.index_source == "history":
-                    --ref_file=$seq_data.seq_source.ref_file
+                    --ref_file '$seq_data.seq_source.ref_file'
                 #else:
-                    --index=${seq_data.seq_source.index.fields.path}
+                    --index '${seq_data.seq_source.index.fields.path}'
                 #end if
             #end if
             
@@ -40,7 +40,7 @@
             #end if 
 
             ## Outputs.
-            --combined-transcripts=${transcripts_combined}
+            --combined-transcripts '${transcripts_combined}'
 
             @CUFFLINKS_GTF_INPUTS@
     </command>