# HG changeset patch
# User ynewton
# Date 1358472127 18000
# Node ID 28d795d45ca2304c72ddc23b6669745ef0b7e476
# Parent  82e5ee13fe5a99e7b65b4808ef67b486fb220863
Uploaded

diff -r 82e5ee13fe5a -r 28d795d45ca2 get_normal_vs_tumor_sample_ids.xml
--- a/get_normal_vs_tumor_sample_ids.xml	Thu Jan 17 20:18:46 2013 -0500
+++ b/get_normal_vs_tumor_sample_ids.xml	Thu Jan 17 20:22:07 2013 -0500
@@ -1,6 +1,6 @@
-<tool id="extract_tumor_vs_normal_ID_lists" name="Extract tumor vs. normal TCGA IDs" version="1.0.0">
+<tool id="extract_tumor_vs_normal_ID_lists" name="Extract_tumor_vs_normal_TCGA_IDs" version="1.0.0">
   <description>Extract normal vs. tumor IDs for TCGA samples</description>
-  <command interpreter="python">get_normal_vs_tumor_sample_ids.py $tableData $outfile1 $outfile2
+  <command interpreter="python">get_normal_vs_tumor_sample_ids.py --in_matrix $tableData --out_normals $outfile1 --out_tumor $outfile2
   </command>
   <inputs>
 	  <param name="tableData" format="tabular" type="data" label="Input data"/>