diff cluster.tools/ipl.feature.selection.xml @ 0:0decf3fd54bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/ipl.feature.selection.xml	Thu Feb 28 01:45:39 2013 -0500
@@ -0,0 +1,83 @@
+<tool id="ipl_feature_selection" name="IPL Feature Selection" force_history_refresh="True">
+    <command interpreter="python">ipl.feature.selection.py
+-d $dataset 
+${genes_only}
+-o ${output}
+
+#if str($thresh_format.format) == 'manual':
+-f ${thresh_format.filter} 
+-t ${thresh_format.threshold} 
+-p ${thresh_format.perc_pass} 
+#end if
+#if str($thresh_format.format) == 'empirical':
+-e ${empirical_fname} 
+#end if
+
+</command>
+    <inputs>
+    	<param name="dataset" type="data" format='tabular' label="Data Set"/>
+    	<param name="genes_only" type="boolean" label="Genes Only (check to set yes)" truevalue="-g" falsevalue="" checked="False" />
+    	
+	<conditional name="thresh_format" >
+	  <param name="format" type='select' label="Input Format for Threshold Used" >
+	    <option value="empirical" selected='true'>Output from the Determine Threshold Tool</option>
+	    <option value="manual">Manually Specify the Threshold</option>
+	  </param>
+	  <when value="manual" >
+	    <param name="filter" type="select" label="Activity Filter" >
+	      <option value="modulated" select='true' >Modulated</option>
+	      <option value="active">Active</option>
+	      <option value="inactive">Inactive</option>
+	    </param>
+	    <param name="perc_pass" type="float" label="% of Samples Passing (value in 0-1 range; >= 1 to indicate exact number of samples)" value="0.33"/>
+	    <param name="threshold" type="float" label="Activity Threshold" value="0.25"/>
+	  </when>
+	  <when value="empirical" >
+	    <param name="empirical_fname" type="data" format='rdata' label="Activity Threshold File" />
+	  </when>
+	</conditional>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="Filtered IPLs"/>
+    </outputs>
+<help>
+.. class:: infomark
+     
+**IPL Feature Selection** - Tool to filter an IPL matrix to contain only those features that exceed a given threshold for a specified percentage of samples
+
+**OUTPUT:**  A new matrix containing only the feaures that pass the user-specified filter
+
+----
+
+**Parameters**
+
+- **Genes Only** Check to limit the new matrix to only gene features
+
+- **Input Format for Threshold Used:** - Specify the format to specify the Threshold.  Choice of:
+         * Output from the 'Determine Threshold Tool'
+         * Manually Specify the Threshold
+
+- **IF Output from the 'Determine Threshold Tool' IS SELECTED:**
+         * **Activity Threshold File** Specify the result file from the 'Determine IPL Threshold for Consensus Clustering" tool
+
+- **IF Manually Specify the Threshold IS SELECTED:**
+         * **Activity Filter** Specify the filter type to use.  Choice of:
+
+                 * Activity -  Features must exceed the user-specified threshold
+                 * Inactivity -  Features must fall below the user-specified threshold
+                 * Modulated - Absolute value of the features must exceed the specified threshold
+
+         * **Percentage of Samples Passing** Percent of samples with an IPL that passes the threshold. Choice of:
+
+                 * Real Value in [0,1] - indicate the percentage of samples that pass the threshold
+                 * Integer Value       - indicate the exact number of samples that pass the threshold
+
+         * **Selection Criteria** Specify the test statistic to use to select the threshold.  Choice of:
+
+                 * Binomial P-value - Select the threshold with the largest -log p-value (calculated as a binomial)
+                 * Chi-Squared P-value - Select the threshold with the largest -log p-value (calculated as a Chi-squared)
+                 * Overall Max Number of Differences - Select the threshold with the largest overall number of differences between the real and null distributions
+
+
+</help>
+</tool>