diff cluster.tools/gen.survival.curves.xml @ 2:b442996b66ae draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/gen.survival.curves.xml	Wed Feb 27 20:17:04 2013 -0500
@@ -0,0 +1,62 @@
+<tool id="gen_survival_curve" name="Generate Kaplan-Meiers Plot for Cluster Result" force_history_refresh="True">
+    <command interpreter="python">gen.survival.curves.py
+-C ${cluster_cls}
+-S ${survial_data}
+-M ${mode}
+-T "${title}"
+-I ${image_format_cond.image_format}
+#if str($image_format_cond.image_format) == 'png':
+-O $report_png
+#end if
+#if str($image_format_cond.image_format) == 'pdf':
+-O $report_pdf
+#end if
+</command>
+<inputs>
+  <param name="cluster_cls" type="data" format="rdata" label="Clustering Classification" help="Specify the clustering classification (must be RData file, see help)"/>
+  <param name="survial_data" type="data" format="tabular" label="Clinical Data" help="Specify the clinical data to use for the Kaplan-Meiers Plot (see help)"/>
+  <param name="mode" type="select" display='radio' label="Report Mode" help="Specify the mode to use when performing Log-Rank tests">
+    <option value="all" selected='true' >All</option>
+    <option value="one">One</option>
+    <option value="both">Both</option>
+  </param> 
+  <conditional name="image_format_cond">
+    <param name="image_format" type="select" display='radio' label="Image format" help="">
+      <option value="pdf">PDF</option>
+      <option value="png" selected='true' >PNG (html wrapper)</option>
+    </param>
+  </conditional>
+
+  <param name="title" type="text" label="Title" value="Report" help="Specify title to use in Kaplan-Meiers Plot"/>
+</inputs>
+<outputs>
+  <data format="png" name="report_png" label="Kaplan-Meier Survival Plot (PNG)">
+    <filter>(image_format_cond['image_format']=="png")</filter>
+  </data>
+  <data format="pdf" name="report_pdf" label="Kaplan-Meier Survival Plot (PDF)">
+    <filter>(image_format_cond['image_format']=="pdf")</filter>
+  </data>
+</outputs>
+<help>
+.. class:: infomark
+     
+**Generate a Kaplan-Meiers Plot for a given cluster result**
+
+----
+
+**Parameters**
+
+- **Clustering Classification** Specify the clustering classification (RData file format - use the 'Convert tab-delimited Cluster Assignments to RData" tool to convert assignments in tab-delimited format).
+
+- **Clinical Data** Clinical data to use for the Kaplan-Meiers Plot (must be formated - See the "Format Raw TCGA sample IDs")
+
+- **Report Mode** Mode to use when performing Log-Rank tests **(MUST SPECIFY A PROPERLY FORMATTED CLINICAL DATA FILE)** .  Choice of:
+
+         * All - All clusters versus each other
+         * One - One cluster versus a meta-cluster composed of the others.  Search performed exhaustively.
+         * Both - Perform both all-v-all and and one-v-others test; select the choice of K that gives the best
+
+- **Title** - Title to use for Kaplan-Meiers Plot
+
+</help>
+</tool>