diff cluster.tools/format.raw.TCGA.RNASeq.data.xml @ 1:dddfeedb85af draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/format.raw.TCGA.RNASeq.data.xml	Fri Mar 01 10:16:53 2013 -0500
@@ -0,0 +1,34 @@
+<tool id="format_raw_TCGA_RNASeq_data" name="Format Raw TCGA RNASeq Data" force_history_refresh="True">
+    <command interpreter="python">format.raw.TCGA.RNASeq.data.py
+-d $dataset
+-l {$log_transform}
+-f ${filter_low_variant}
+-o ${output}
+
+</command>
+    <inputs>
+    	<param name="dataset" type="data" format='tabular' label="Raw TCGA RNASeq Data"/>
+        <param name="log_transform" type='select' display="radio" label="Log-transform data?" help="Specify whether or not to log-transform the data matrix (log(x+1))">
+          <option value="no">No</option>
+          <option value="yes" selected='true' >Yes</option>
+        </param>
+        <param name="filter_low_variant" type='integer' label="Filter Threshold for Low-variant genes?" value="10" help="Specify threshold for minimum median value for all genes (-1 to use no filter)">
+          <option value="yes" selected='true' >Yes</option>
+          <option value="no">No</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="Formatted RNASeq Data"/>
+    </outputs>
+<help>
+.. class:: infomark
+     
+**Format Raw TCGA RNASeq Data** - Tool to convert a raw RNASeq TCGA data file (a file from either Synapse or Firehose) into a the format expected by the Survival Analysis tools
+
+**Log-transform data?** -Specify whether or not to log-transform the data matrix.  To avoid numeric underflow, this will use log(x+1), where x is the value of the RNASeq data
+
+**OUTPUT:**  A new tab-delimited file containing the log-transformed RNASeq data
+
+</help>
+</tool>