comparison computeMatrix.xml @ 13:b4c5dd45778a draft

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12:aea72b24dea0

        <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>

    
    </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>

13:b4c5dd45778a

        <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="input_graphic_output_settings">
        <expand macro="input_save_matrix_values" />
    </expand>

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

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