diff cluster.tools/gen.matrix.heatmap.xml @ 0:0decf3fd54bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/gen.matrix.heatmap.xml	Thu Feb 28 01:45:39 2013 -0500
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+<tool id="gen_matrix_heatmap" name="Generate Heatmap for Matrix" force_history_refresh="True">
+  <command interpreter="python">gen.matrix.heatmap.py
+-d ${dataset1}
+-i ${image_format_cond.image_format}
+-t ${output_treeview_format}
+-r ${reverse_rows}
+
+#if str($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 $report_pdf
+#end if
+#if str($treeview_output) != 'None':
+-o ${treeview_output}
+#end if
+
+</command>
+<inputs>
+  <param format="tabular" name="dataset1" type="data" label="Data Matrix" help="Provide a tab-delimited file with data to put into a heatmap generate"/>
+  <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 data matrix (HTML)">
+    <filter>(image_format_cond['image_format']=="png")</filter>
+  </data>
+  <data format="pdf" name="report_pdf" label="Heatmap from data matrix (PDF)">
+    <filter>(image_format_cond['image_format']=="pdf")</filter>
+  </data>
+  <data format="tgz" name="treeview_output" label="Heatmap from data matrix (tgz of TreeView files)">
+    <filter>(output_treeview_format)=="yes"</filter>
+  </data>
+</outputs>
+<help>
+.. class:: infomark
+     
+**Generate Heatmap for Matrix** - Tool to Generate a simple heatmap for a data matrix 
+- The tool uses HAC, with euclidean distance.  If user wants other options, we recomend using either the:
+
+      * Consensus Clustering tool
+      * Hierarchcical Clustering tool, OR
+      * Partitition Clusterint tool
+
+**OUTPUT:**  
+      * **Heatmap** in either PDF or PNG format
+      * **TreeView Files**  gzip tarball file of the relevant files (OPTIONAL)
+
+----
+
+**Parameters**
+
+- **Matrix in tab-delimited format** Tab-delimited file
+
+</help>
+</tool>