comparison computeMatrix.xml @ 10:135f3bae5c56 draft

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9:c53a73b8eef9

<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0">
    <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
    <expand macro="requirements" />
    <macros>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        #import tempfile

      </when>
      
      <when value="reference-point">
        <param name="referencePoint" type="select" label="The reference point for the plotting">
            <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
            <option value="TES">end of region (e.g. TES)</option>
            <option value="center">center of region</option>
        </param>
        
        <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" label="Discard any values after the region end" help="This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the TSS."/>
        <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/>
        
        <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
      </when>
    </conditional>
    
    <conditional name="output" >
        <param name="showOutputSettings" type="select" label="Show additional output options" >
            <option value="no" selected="true">no</option>
            <option value="yes">yes</option>
        </param>
          <when value="no" />
          <when value="yes">
            <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/>
            <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/>
            <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
        </when>
    </conditional>

    <conditional name="advancedOpt" >
      <param name="showAdvancedOpt" type="select" label="Show advanced options" >
        <option value="no" selected="true">no</option>
        <option value="yes">yes</option>

      </when>
    </conditional>
    
    </inputs>
  <outputs>
    <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix">
    </data>
    <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
        <filter>
        ((
            output['showOutputSettings'] == 'yes' and 
            output['saveData'] is True
        ))
        </filter>
    </data>
    <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
        <filter>
        ((
            output['showOutputSettings'] == 'yes' and 
            output['saveMatrix'] is True
        ))
        </filter>
    </data>
    <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
        <filter>
        ((
            output['showOutputSettings'] == 'yes' and 
            output['saveSortedRegions'] is True
        ))
        </filter>
    </data>
  </outputs>
    <!--
    computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 
    -->
    <tests>

10:135f3bae5c56

<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.2">
    <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        #import tempfile

      </when>
      
      <when value="reference-point">
        <param name="referencePoint" type="select" label="The reference point for the plotting">
            <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
            <option	 value="TES">end of region (e.g. TES)</option>
            <option value="center">center of region</option>
        </param>
        
        <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" label="Discard any values after the region end" help="This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the TSS."/>
        <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/>
        
        <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
      </when>
    </conditional>

    <expand macro="graphic_output_settings" />

    <conditional name="advancedOpt" >
      <param name="showAdvancedOpt" type="select" label="Show advanced options" >
        <option value="no" selected="true">no</option>
        <option value="yes">yes</option>

      </when>
    </conditional>
    
    </inputs>
  <outputs>
    <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
    <expand macro="output_graphic_outputs" />
  </outputs>
    <!--
    computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 
    -->
    <tests>