diff bamPEFragmentSize.xml @ 65:9bee2c86eeb1 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty

--- a/bamPEFragmentSize.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/bamPEFragmentSize.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
-    <description>Given a BAM file it samples several regions to estimate the paird-end fragment length</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
+    <description>Given a BAM file it samples several regions to estimate the paired-end fragment length</description>
     <macros>
         <token name="@BINARY@">bamPEFragmentSize</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         bamPEFragmentSize
@@ -16,8 +15,6 @@
             #end if
             '$bamInput'
             > $outfile
-        &&
-        mv ./hist.png $histogram_outfile
 ]]>
     </command>
     <inputs>
@@ -29,7 +26,7 @@
     </inputs>
     <outputs>
         <data name="outfile" format="txt"/>
-        <data name="histogram_outfile" format="png">
+        <data name="histogram_outfile" from_work_dir="hist.png" format="png">
             <filter>histogram is True</filter>
         </data>
     </outputs>