Mercurial > repos > melissacline > ucsc_cancer_utilities

diff segToGeneMatrix.xml @ 54:59dbe857f5d4

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introduce normal_CNV parameter
author jingchunzhu
date Thu, 17 Sep 2015 22:03:04 -0700
parents 728eda331f07
children 2a240b005731
line wrap: on
line diff
--- a/segToGeneMatrix.xml	Thu Sep 17 15:38:53 2015 -0700
+++ b/segToGeneMatrix.xml	Thu Sep 17 22:03:04 2015 -0700
@@ -3,7 +3,7 @@
     Convert segmented copy number data to gene-level matrix data
   </description>
   <command interpreter="python">
-    seg2matrix/mapSegToGeneMatrix.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix
+    seg2matrix/mapSegToGeneMatrix.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix $normal_CNV_value
   </command>
   <inputs>
     <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" help="See input data format section for required input format" />
@@ -18,7 +18,8 @@
       <when value="hg18">
         <param name="assembly" type="hidden" value="refGene_hg18" />
       </when>
-    </conditional>  
+    </conditional>
+    <param name="normal_CNV_value" type="text" value="0" lable="what is the value to represent normal copy number" />
   </inputs>
   <outputs>
     <data name="outputMatrix" format="tabular" label="gene-level copy number matrix" />