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

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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>