diff cluster.tools/fix.and.merge.TCGA.sample.IDs.xml @ 2:b442996b66ae draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/fix.and.merge.TCGA.sample.IDs.xml	Wed Feb 27 20:17:04 2013 -0500
@@ -0,0 +1,33 @@
+<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}
+-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)"/>
+    </outputs>
+<help>
+.. class:: infomark
+     
+**Update and Merge TCGA Sample IDs** - This will limit the TCGA sample IDs to the specified numnber of elements (min is 3).  If necessary, samples will be merged (by averaging)
+
+**OUTPUT:**  A new matrix using sample (columns) that use the specified number of components
+
+----
+
+**Parameters**
+
+- **Matrix with TCGA barcode sample IDs (e.g. TCGA-AE-####-01-)** Specify a data matrix with TCGA barcodes
+
+- **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>