Mercurial > repos > bgruening > deeptools

diff correctGCBias.xml @ 66:1dbd76a58d8b draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
author galaxyp
date Sat, 30 May 2015 13:55:46 -0400
parents 9bee2c86eeb1
children
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line diff
--- a/correctGCBias.xml	Mon May 25 05:16:10 2015 -0400
+++ b/correctGCBias.xml	Sat May 30 13:55:46 2015 -0400
@@ -26,7 +26,9 @@
             #if str($region).strip() != '':
                 --region '$region'
             #end if
-            --correctedFile $outFileName
+            --correctedFile corrected.bam;
+
+        mv corrected.bam $outFileName;
 ]]>
     </command>
     <inputs>
@@ -43,12 +45,12 @@
     <tests>
         <test>
             <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
-            <param name="bamInput" value="phiX.bam" ftype="bam" />
+            <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
             <param name="ref_source" value="history" />
-            <param name="input1" value="phiX.2bit" />
+            <param name="input1" value="sequence.2bit" />
             <param name="effectiveGenomeSize_opt" value="specific" />
-            <param name="effectiveGenomeSize" value="5386" />
-            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" compare="sim_size" />
+            <param name="effectiveGenomeSize" value="23011544" />
+            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" />
         </test>
     </tests>
     <help>