diff cluster.tools/heatmap.from.cluster.result.xml @ 2:b442996b66ae draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/heatmap.from.cluster.result.xml	Wed Feb 27 20:17:04 2013 -0500
@@ -0,0 +1,124 @@
+<tool id="cluster_heatmap" name="Generate Heatmap for Clustering Result" force_history_refresh="True">
+  <command interpreter="python">heatmap.from.cluster.result.py
+-d ${dataset1}
+-s ${cluster_second_direction_cond.cluster_second_direction}
+
+#if str($cluster_second_direction_cond.cluster_second_direction) == 'prev':
+-D ${cluster_second_direction_cond.dataset2}
+#end if
+-i ${image_format_cond.image_format}
+-t ${output_treeview_format}
+-r ${reverse_rows}
+#if str($plot_kms_cond.plot_kms) == 'yes':
+-C ${dataset1}
+-S ${plot_kms_cond.survial_data}
+-M ${plot_kms_cond.mode}
+-T "${plot_kms_cond.title}"
+-I none
+#end if
+
+#if str($image_format_cond.image_format) == 'png':
+-h $report_html
+-p ${report_html.files_path}
+#end if
+#if str($image_format_cond.image_format) == 'pdf':
+-h $report_pdf
+-p ${report_pdf.files_path}
+#end if
+#if str($treeview_output) != 'None':
+-o ${treeview_output}
+#end if
+
+</command>
+<inputs>
+  <param format="rdata" name="dataset1" type="data" label="Clustering Classification" help="Cluster result file from CCPLUS, HAC, or PAM"/>
+  <conditional name="plot_kms_cond">
+    <param name="plot_kms" type='select' label="Plot Kaplan-Meiers Survival Plot as well (primary clustering ONLY)?" >
+      <option value="no" selected='true'>No</option>
+      <option value="yes" >Yes</option>
+    </param>
+    <when value='yes'>
+      <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 (see help below)">
+	<option value="all" selected='true' >All</option>
+	<option value="one">One</option>
+	<option value="both">Both</option>
+      </param> 
+      <param name="title" type="text" label="Title" value="Report"/>
+    </when>
+  </conditional>
+  <conditional name="cluster_second_direction_cond">
+    <param name="cluster_second_direction" type="select" label="Cluster the second dimension? (e.g. rows if this is a sample cluster)"  help="Cluster the 2nd dimension of matrix in the cluster result (see help below)">
+      <option value="no" selected="true">No</option>
+      <option value="yes">Yes</option>
+      <option value="prev">Previous Cluster Result</option>
+    </param>
+    <when value="prev">
+      <param format="rdata" name="dataset2" type="data" label="Previous Cluster result #2 (secondary result, e.g. rows)" help="Cluster result file from CCPLUS, HAC, or PAM"/>
+    </when>
+  </conditional>
+  <conditional name="image_format_cond">
+    <param name="image_format" type="select" display='radio' label="Image format">
+      <option value="pdf">PDF</option>
+      <option value="png" selected='true' >PNG (html wrapper)</option>
+    </param>
+  </conditional>
+  <param name="output_treeview_format" type='select' display="radio" label="Output in TreeView format as well?" help="Specify whether or not to produce files for TreeView" >
+    <option value="no">No</option>
+    <option value="yes" selected='true' >Yes</option>
+  </param>
+  <param name="reverse_rows"  type='select'  display="radio" label="Reverse Row-order (to make consistent w\TreeView Display)?" help="Specify whether or not to reverse Row-order (to make the heatmap consistent with output from TreeView (reversed otherwise)" >
+    <option value="no" selected='true'>No</option>
+    <option value="yes">Yes</option>
+  </param>
+</inputs>
+<outputs>
+  <data format="html" name="report_html" label="Heatmap from cluster results (HTML)">
+    <filter>(image_format_cond['image_format']=="png")</filter>
+  </data>
+  <data format="pdf" name="report_pdf" label="Heatmap from cluster results (PDF)">
+    <filter>(image_format_cond['image_format']=="pdf")</filter>
+  </data>
+  <data format="tgz" name="treeview_output" label="Heatmap from cluster results (tgz of TreeView files)">
+    <filter>(output_treeview_format)=="yes"</filter>
+  </data>
+</outputs>
+<help>
+.. class:: infomark
+     
+**Generate Heatmap for Clustering Result** - Tool to generate a heatmap and dendrogram for a clustering result
+
+**OUTPUT:**  
+      * **Heatmap** in either PDF or PNG format
+      * **TreeView Files**  gzip tarball file of the relevant files (OPTIONAL)
+
+----
+
+**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).
+
+- **Plot Kaplan-Meiers Survival Plot as well (primary clustering ONLY)?** Specify whether or not to also plot a Kaplan-Meiers Surivial Plot.  **NOTE*, the cluster results must be a **SAMPLE** cluster.
+ 
+- **Cluster the second dimension?** Specify whether or not to cluster the 2nd dimension of matrix in the cluster result.  Choice of:
+         * No
+         * Yes - Generate a default clustering (HAC with Euclidean distance)
+         * Previous Cluster Result - MUST specify a previous clustering result
+
+- **IF Cluster the second dimension? is a previous clustering result:**
+         * **Previous Cluster result #2** Specify the clustering classification for the 2nd dimension (RData file format - use the 'Convert tab-delimited Cluster Assignments to RData" tool to convert assignments in tab-delimited format).
+
+- **IF Plot Kaplan-Meiers Survival Plot is YES:**
+         * **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>