comparison cluster.tools/heatmap.from.cluster.result.xml @ 3:563832f48c08 draft

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2:b8f262149ee2

</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="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>

      <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>

      <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>

3:563832f48c08

</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>

      <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>

      <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>