diff segToMatrix.xml @ 32:8e888e966c47

change segToMatrix.xml location

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segToMatrix.xml	Fri Jul 24 14:09:57 2015 -0700
@@ -0,0 +1,37 @@
+<tool id="segToMatrix" name="segToMatrix" version="0.0.1">
+  <description>
+    Prep segmented copy number data for Xena
+  </description>
+  <command interpreter="python">
+    seg2matrix/segToMatrixGalaxy.py $input seg2matrix/$refGene.assembly $outputMatrix $outputProbeMap
+  </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="xena copy number matrix" />
+    <data name="outputProbeMap" format="tabular" label="associated probemap"/>
+  </outputs>
+  <help>
+    ***Convert segmented copy number data for input into xena***
+
+    Given a segmented copy number data file, convert it into xena ready data files.
+
+    File no 1. matrix file
+
+    File no 2. probeMap file -- probe to gene mapping file  (is in the same genome assembly as the input segmented copy number data)
+  </help>
+</tool>
+