view cluster.tools/heatmap.from.cluster.result.xml @ 6:3d3a8595b981 draft

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<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}
-k ${plot_kms_cond.plot_kms}
#if str($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)?" help="NOTE: this only works when the Image Format is PNG.  For a PDF of the KM plot, you can use the 'Generate Kaplan-Meiers Plot for Cluster Result' tool">
      <option value="yes" >Yes</option>
      <option value="no" selected='true'>No</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="yes">Yes</option>
      <option value="no" selected="true">No</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="yes" selected='true' >Yes</option>
    <option value="no">No</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="yes">Yes</option>
    <option value="no" selected='true'>No</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>