diff cluster.tools/rnaseq.feature.selection.xml @ 1:dddfeedb85af draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/rnaseq.feature.selection.xml	Fri Mar 01 10:16:53 2013 -0500
@@ -0,0 +1,52 @@
+<tool id="rnaseq_feature_selection" name="RNASeq Feature Selection" force_history_refresh="True">
+    <command interpreter="python">rnaseq.feature.selection.py
+-d $dataset 
+-z ${z_transform}
+-m ${var_method} 
+-p ${perc_pass} 
+-o ${output}
+
+</command>
+    <inputs>
+    	<param name="dataset" type="data" format='tabular' label="RNASeq Data Set"/>
+        <param name="z_transform" type='select' display="radio" label="Z-transform data?" help="Specify whether or not to Z-transform the rows (mean=0, sd=1)">
+          <option value="yes" selected='true' >Yes</option>
+          <option value="no">No</option>
+        </param>
+    	<param name="var_method" type="select" label="Variance Metric for Genes" help="Specify Metric to use for calculating Gene Variance" >
+	  <option value="mad">Median Absolute Deviation (MAD)</option>
+	  <option value="maxad">Maximum Absolute Deviation (Max AD)</option>
+	  <option value="sd">Standard Deviation (SD)</option>
+    	</param>
+	<param name="perc_pass" type="float" label="Total number of features to keep" help="Use value >= 1 to indicate exact number of genes. Use value in 0-1 range to specify percentage" value="1500"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="Filtered RNASeqs"/>
+    </outputs>
+<help>
+.. class:: infomark
+     
+**RNASeq Feature Selection** - Tool to filter an RNASeq matrix to select the most variant features
+
+**OUTPUT:**  A new matrix containing only the most variant feaures
+
+----
+
+**Parameters**
+
+- **Z-transform data?** - Specify whether or not to Z-transform the rows (mean=0, sd=1)
+- **Variance Metric for Genes** - Specify Metric to use for calculating Gene Variance. Choice of:
+
+	 * Median Absolute Deviation (MAD)
+	 * Maximum Absolute Deviation - similar to MAD, but uses the _Maximum_, instead of the Median Absolute Deviatioin
+	 * Standard Deviation
+
+ - **Percentage of Samples Passing** Percent of samples with an IPL that passes the threshold. Choice of:
+
+         * Integer Value       - indicate the exact number of genes that are to be kept
+         * Real Value in [0,1] - indicate the percentage of genes that are to be kept
+
+
+
+</help>
+</tool>