diff cluster.tools/fix.and.merge.TCGA.sample.IDs.xml @ 3:563832f48c08 draft

Uploaded

--- a/cluster.tools/fix.and.merge.TCGA.sample.IDs.xml	Fri Mar 01 10:17:24 2013 -0500
+++ b/cluster.tools/fix.and.merge.TCGA.sample.IDs.xml	Fri Mar 01 19:51:25 2013 -0500
@@ -1,13 +1,13 @@
 <tool id="fix_and_merge_TCGA_samples_IDs" name="Fix and Merge TCGA sample IDs" force_history_refresh="True">
     <command interpreter="python">fix.and.merge.TCGA.sample.IDs.py
--d $dataset -n ${num_components} ${remove_normals}
+-d $dataset 
+-n ${num_components}
 -o ${output}
 
 </command>
     <inputs>
     	<param name="dataset" type="data" format='tabular' label="Matrix with Full TCGA Aliquot Barcodes"/>
 	<param name="num_components" type="integer" label="Number of barcode components to use (min number is 3)" value="3" />
-	<param name="remove_normals" type="boolean" label="Remove Normals from Matrix? (check to exclude)" truevalue="-r" falsevalue="" checked="True" />
     </inputs>
     <outputs>
         <data format="tabular" name="output" label="Matrix with TCGA Patient Barcodes (filtered and merged)"/>
@@ -27,7 +27,5 @@
 
 - **Number of barcode components to use** Specify the number of barcode components to use in new matrix that is produced **(min number is 3)**
 
-- **Remove Normals from Matrix?** - Remove any normals from the matrix (if necessary)
-
 </help>
 </tool>