annotate dsCompareCurves.xml @ 0:cbeae0f83ff8 draft

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<tool id="deepstats_compare_curves" name="dsCompareCurves" version="@WRAPPER_VERSION@.0" profile="18.01">
    <description>
        compares multiple bigwigs over multiple region sets with bootstraps and
        Wilcoxon rank-sum test using deepTools computeMatrix output
    </description>
    <macros>
        <token name="@BINARY@">dsCompareCurves</token>
        <import>deepStats_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
     <![CDATA[
      @BINARY@
        --input '$input'
        --output 'output'
        --comparison '$comparison'
        --signalName '$signalName'
        --scoreLabels '$nameLabels.scoreLabels'
        --regionLabels '$nameLabels.regionLabels'

        #if $scaleRegions.showScaleRegionsOpt == "yes":
          --firstRegionName '$scaleRegions.firstRegionName'
          --secondRegionName '$scaleRegions.secondRegionName'
        #else
          --firstRegionName '$scaleRegions.firstRegionName'
        #end if

        --bootstraps '$statsOptions.bootstraps'
        --bootstrapsCI '$statsOptions.bootstrapsCI'
        --wilcoxThreshold '$statsOptions.wilcoxThreshold'
        --bootPlotShareY '$plotOptions.bootPlotShareY'
        --bootPlotRatio '$plotOptions.bootPlotRatio'
        --bootPlotWidth '$plotOptions.bootPlotWidth'
        --bootPlotHeight '$plotOptions.bootPlotHeight'
        --wilcoxPlotWidth '$plotOptions.wilcoxPlotWidth'
        --wilcoxPlotHeight '$plotOptions.wilcoxPlotHeight'
        --CPU '$advancedOptions.CPU'

        #if $fontOptions.showFontOptions == "yes":
          --font '$fontOptions.font_file'
        #end if

        #if $colorsOptions.showColorsOptions == "yes":
          --bootPlotColors '$colorsOptions.bootPlotColors'
        #end if
    ]]>
    </command>
    <inputs>
      <param argument="--input" format="tabular" type="data"
        label="deepTools computeMatrix output file."/>

      <param argument="--comparison" type="select"
        label="What do you want to compare?">
        <option value="scores" selected="true">scores</option>
        <option value="regions">regions</option>
      </param>

      <param argument="--signalName" type="text" value= "Normalized ATAC-seq counts"
        label="Name of the genomic signal" help="Name given to the signal on the plots, \n can be added for linebreaks."/>

      <conditional name="scaleRegions">
          <param name="showScaleRegionsOpt" type="select" label="Which mode was used in deepTools computeMatrix?">
            <option value="reference-point" selected="true">reference-point</option>
            <option value="scale-regions">scale-regions</option>
          </param>
          <when value="scale-regions">
            <param argument="--firstRegionName" type="text" value="TSS" size="10"
                      label="Label for the region start"
                      help ="Label shown in the plot
                      for the start of the region. Default is TSS (transcription start site),
                      but could be changed to anything, e.g. &quot;peak start&quot;." />
            <param argument="--secondRegionName" type="text" value="TES" size="10"
                      label="Label for the region end"
                      help ="Label shown in the plot
                      for the end of the region. Default is TES (transcription end site),
                      but could be changed to anything, e.g. &quot;peak end&quot;." />
          </when>
          <when value="reference-point">
            <param argument="--firstRegionName" type="text" value="TSS"
                      label="Label for the region start"
                      help ="Label shown in the plot
                      for the start of the region. Default is TSS (transcription start site),
                      but could be changed to anything, e.g. &quot;peak start&quot;." />
          </when>
      </conditional>

      <section name="nameLabels" title="Customize score and region labels" expanded="false">
          <param argument="--scoreLabels" optional="true" type="text" value= ""
          label="Name of the scores" help="For plot display. It must be provided as text seperated
          by semi-colons, i.e. 'Score A;Score B;Score C' as in the example.">
            <sanitizer>
              <valid initial="string.printable"/>
            </sanitizer>
          </param>

          <param argument="--regionLabels" optional="true" type="text" value= ""
          label="Name of the regions" help="For plot display. It must be provided as text seperated
          by semi-colons, i.e. 'Regions A;Regions B;Regions C' as in the example.">
          <sanitizer>
            <valid initial="string.printable"/>
          </sanitizer>
        </param>
      </section>

      <section name="statsOptions" title="Statistics options" expanded="false">
          <param argument="--bootstraps" type="integer" value="1000"
          label="--bootstraps" help="Number of bootstraps to perform. Default is 1000,
          increasing this number will increase the computing time."/>
          <param argument="--bootstrapsCI" type="float" value="0.95"
          label="--bootstrapsCI" help="Bootstraps confidence interval. Default is 0.95,
          increasing this will make the analysis more stringent by increasing            the min and max of the shadowed area on the bootstrap plot."/>
          <param argument="--wilcoxThreshold" type="float" value="0.05"
          label="--wilcoxThreshold" help="Threshold used to define significant
          bins on the Wilcoxon rank-sum test plot (grey box). Default is 0.05"/>
      </section>

      <section name="plotOptions" title="Plotting options" expanded="false">
        <param argument="--bootPlotShareY" type="select" label="--bootPlotShareY">
          <option value="TRUE" selected="true">TRUE</option>
          <option value="FALSE">FALSE</option>
        </param>
        <param argument="--bootPlotRatio" type="float" value="0.85" label="--bootPlotRatio"
        help="Changes the aspect ratio of the plot. A value inferior to 1 results in a wide plot,
        a value above 1 results in a narrow plot. Default: 0.85."/>

        <param argument="--bootPlotWidth" type="float" value="5.2" label="--bootPlotWidth"
        help="How large the bootstraps plot should be."/>

        <param argument="--bootPlotHeight" type="float" value="3.7" label="--bootPlotHeight"
        help="How tall the bootstraps plot should be."/>

        <param argument="--wilcoxPlotWidth" type="float" value="4.6" label="--wilcoxPlotWidth"
        help="How large the Wilcoxon rank-sum test plot should be."/>

        <param argument="--wilcoxPlotHeight" type="float" value="4.6" label="--wilcoxPlotHeight"
        help="How tall the Wilcoxon rank-sum test  plot should be."/>
      </section>

      <section name="advancedOptions" title="Computing options" expanded="false">
        <param argument="--CPU" type="integer" value="4" label="--CPU"
        help="Number of CPU to use."/>
      </section>

      <conditional name="fontOptions">
        <param name="showFontOptions" type="select" label="Customize font?">
          <option value="No" selected="true">No</option>
          <option value="Yes">Yes</option>
        </param>
        <when value="No"/>
        <when value="Yes">
          <param argument="--font" type="file" format="ttf" value=" " label="--font" optional="true"
          help="Font used for plotting, given a TTF file. Default is usually Helvetica."/>
        </when>
      </conditional>

      <conditional name="colorsOptions">
        <param name="showColorsOptions" type="select" label="Customize colors?">
          <option value="No" selected="true">No</option>
          <option value="Yes">Yes</option>
        </param>
        <when value="No"/>
        <when value="Yes">
          <param argument="--bootPlotColors" type="file" format="tabular" value=" " label="--bootPlotColors"
          help="Change the bootstraps plot color palette to a user-provided one. The file must
          be tab-delimited and contain for each line two HTML color codes ( #3366CC   #769EF2 ).
          The first column corresponds to the mean color, the second column corresponds to the
          color of the bootstrap confidence interval shadowed area. The default color scale
          contains 6 colors that are color blind friendly using the dichromat R package."/>
        </when>
      </conditional>

    </inputs>
    <outputs>
      <data format="pdf" name="pdf1" label="${tool.name} on ${on_string}: Bootstrap Plot" from_work_dir="output_bootstraps.pdf"/>
      <data format="pdf" name="pdf2" label="${tool.name} on ${on_string}: Wilcox Plot" from_work_dir="output_wilcoxon.pdf"/>
    </outputs>
    <tests>
      <test>
      </test>
    </tests>
    <help>
      <![CDATA[
      This tool assesses if multiple genomics signals ( ChIP-seq, ATAC-seq... ) are significantly different or
      not between conditions ( control, KO1, KO2, etc ). `dsCompareCurves` uses bootstraps and corrected
      Wilcoxon Rank-sum tests to do so. The input of this tool corresponds to the output of deepTools
      `computeMatrix --outFileNameMatrix`. If multiple region sets have been used in deepTools, one plot and
      tab-delimited table will be produced for each set of regions.

      @REFERENCES@
      ]]>
    </help>
    <expand macro="citations" />
</tool>