diff cuffmerge_wrapper.xml @ 14:6a6717a5f421 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"

--- a/cuffmerge_wrapper.xml	Sun Feb 19 12:12:38 2017 -0500
+++ b/cuffmerge_wrapper.xml	Tue Jun 16 13:00:53 2020 -0400
@@ -1,14 +1,16 @@
-<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.1">
+<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.2">
     <description>merge together several Cufflinks assemblies</description>
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-     <version_command>cuffmerge -v</version_command>
-    <command detect_errors="aggressive">
-        python '$__tool_directory__/cuffmerge_wrapper.py'
+    <version_command>cuffmerge -v</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        @CUFFLINKS_LINK_GTF_INPUTS@
+        echo @CUFFLINKS_GTF_INPUTS@ | sed 's/\s\+/\n/' > assembly_GTF_list.txt &&
+        cuffmerge 
+            -o output
             --num-threads="\${GALAXY_SLOTS:-4}"
-            
             ## Use annotation reference?
             #if $annotation.use_ref_annotation == "Yes":
                 -g '${annotation.reference_annotation}'
@@ -25,12 +27,8 @@
             #end if
 
             --min-isoform-fraction="${min_isoform_fraction}"
-
-            ## Outputs.
-            --merged-transcripts '${merged_transcripts}'
-
-            @CUFFLINKS_GTF_INPUTS@
-    </command>
+            assembly_GTF_list.txt
+    ]]></command>
     <inputs>
         <expand macro="cufflinks_gtf_inputs" />
         <conditional name="annotation">
@@ -74,7 +72,7 @@
     </inputs>
 
     <outputs>
-        <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/>
+        <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts" from_work_dir="output/merged.gtf"/>
     </outputs>
 
     <tests>
@@ -127,7 +125,5 @@
 
 Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies.
     </help>
-    <citations>
-        <citation type="doi">10.1038/nbt.1621</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>