diff cluster.tools/determine.IPL.threshold.xml @ 0:0decf3fd54bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/determine.IPL.threshold.xml	Thu Feb 28 01:45:39 2013 -0500
@@ -0,0 +1,57 @@
+<tool id="determine_ipl_threshold" name="Determine IPL Threshold for Consensus Clustering" force_history_refresh="True">
+    <command interpreter="python">determine.IPL.threshold.py
+-d ${data_fname}
+-f ${filter_type}
+-p ${percentage_pass}
+-s ${selection_criteria}
+-h $report 
+-r ${report.files_path}
+-o ${output_rdata}
+    </command>
+    <inputs>
+      <param name="data_fname" type="data" format="tabular" label="Paradigm Results File (contains both reals and nulls)"/>
+      <param name="filter_type" type="select" label="Activity Filter" help="Specify the filter type to use (see help below)">
+	<option value="active">Active</option>
+	<option value="inactive">Inactive</option>
+	<option value="modulated" selected='true' >Modulated</option>
+      </param>
+      <param name="percentage_pass" type="float" label="% of Samples Passing (value in 0-1 range; >= 1 to indicate exact number of samples)" value="0.33" help="Specify the percentage of samples thatmust pass the threshold (see help below)"/>
+      <param name="selection_criteria" type="select" label="Selection Criteria" help="Specify the test statistic to use to select the threshold (see help below)">
+	<option value="binomial">Binomial P-value</option>
+	<option value="chisq">Chi-Squared P-value</option>
+	<option value="max_diffs" selected='true' >Overall Max Number of Differences</option>
+      </param>
+    </inputs>
+    <outputs>
+      <data format="html" name="report" label="Determine IPL Threshold (HTML)"/>
+      <data format="rdata" name="output_rdata"  label="Determine IPL Threshold (RData)"/>
+    </outputs>
+<help>
+
+.. class:: infomark
+     
+**Determines a statistically sound threshold to use for a given IPL result**
+
+**Parameters**
+- **Paradigm Results File** Output from Paradigm (tab-delimited and contains both the 'real' and 'null' samples)
+
+- **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>