diff segToGeneMatrix.xml @ 39:61f03b481b0d

new tool

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segToGeneMatrix.xml	Fri Jul 31 20:38:27 2015 -0700
@@ -0,0 +1,35 @@
+<tool id="segToGeneMatrix" name="segToGeneMatrix" version="0.0.1">
+  <description>
+    Convert segmented copy number data to gene based matrix data
+  </description>
+  <command interpreter="python">
+    seg2matrix/mapSegToGeneMatrix.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix
+  </command>
+  <inputs>
+    <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" />
+    <conditional name="refGene">
+      <param name="assembly_select" type="select" label="Which human genome assembly is your input segmented copy number data?">
+	<option value="hg19">hg19</option>
+	<option value="hg18">hg18</option>
+      </param>
+      <when value="hg19">
+        <param name="assembly" type="hidden" value="refGene_hg19" />
+      </when>
+      <when value="hg18">
+        <param name="assembly" type="hidden" value="refGene_hg18" />
+      </when>
+    </conditional>  
+  </inputs>
+  <outputs>
+    <data name="outputMatrix" format="tabular" label="gene-level copy number matrix" />
+  </outputs>
+  <help>
+    ***Convert segmented copy number data for input into xena***
+
+    Given a segmented copy number data file, convert it into gene based matrix data
+
+    Output File no 1. matrix file
+
+  </help>
+</tool>
+