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

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<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>