diff macs2_refinepeak.xml @ 5:beb902da6e5f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b

--- a/macs2_refinepeak.xml	Mon Feb 06 02:30:37 2017 -0500
+++ b/macs2_refinepeak.xml	Sat Apr 08 08:28:57 2017 -0400
@@ -7,13 +7,15 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command>
+        <![CDATA[
         macs2 refinepeak
-            -b "${ bed_infile }"
-            -i "${ infile }"
+            -b '${ bed_infile }'
+            -i '${ infile }'
             --format '${ infile.extension.upper() }'
-            --cutoff "${ cutoff }"
-            --window-size "${ winsize }"
-            --ofile "${ outfile }"
+            --cutoff '${ cutoff }'
+            --window-size '${ winsize }'
+            --ofile '${ outfile }'
+        ]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
@@ -27,19 +29,24 @@
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="ChIP_200K.bed" ftype="bed"/>
-            <param name="bed_infile" value="callpeak_summits_part.bed" ftype="bed"/>
+            <param name="infile" value="refinepeak_bam_input.bam" ftype="bam"/>
+            <param name="bed_infile" value="refinepeak_bed_input.bed" ftype="bed"/>
             <param name="cutoff" value="5.0"/>
             <param name="winsize" value="200"/>
-            <output name="outfile" file="refinepeak_ChIP_and_summits.bed"/>
+            <output name="outfile" file="refinepeak_output.bed"/>
         </test>
     </tests>
     <help>
+        <![CDATA[
 **What it does**
 
-(Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP.
+This is **refinepeak** utility from the MACS2_ Package. It is an experimental utility that takes raw read alignments, refines peak summits and gives scores measuring balance of forward- backward tags. Inspired by the SPP_ pipeline.
+
+.. _MACS2: https://github.com/taoliu/MACS
+.. _SPP: http://compbio.med.harvard.edu/Supplements/ChIP-seq/
 
 @citation@
+]]>
     </help>
     <expand macro="citations" />
 </tool>