comparison plotwithscale.xml @ 56:9ceb3ffcd817 draft

Uploaded 20170608

55:7698612e1dc7

      </conditional>
    </section>
  </inputs>

  <outputs>
    <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->
    <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.testandplot.adjustedpvalue.txt" />
    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
  </outputs>

  <help>
This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
for the different tests performed at the selected scale, and it creates a graphical representation of the
Interval-Wise Testing results and a summary plot (optional) at the selected scale.

56:9ceb3ffcd817

      </conditional>
    </section>
  </inputs>

  <outputs>
    <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.plotwithscale.stackerr.txt" />-->
    <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" />
    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" />
    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" />
  </outputs>

  <tests>
    <test>
      <param name="rdata" value="output_testandplot/iwtomics.testandplot.RData" ftype="rdata" />
      <param name="testids" value="output_testandplot/iwtomics.testandplot.tests.txt" ftype="tabular" />
      <param name="featureids" value="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" ftype="tabular" />
      <repeat name="thresholdontestscale">
        <param name="test" value="1" />
        <param name="feature" value="1" />
        <param name="scale" value="10" />
      </repeat>
      <repeat name="thresholdontestscale">
        <param name="test" value="1,2,3" />
        <param name="feature" value="2" />
        <param name="scale" value="20" />
      </repeat>
      <param name="alpha" value="0.05" />
      <param name="average" value="TRUE" />
      <param name="size" value="TRUE" />
      <param name="plottype" value="boxplot" />
      <param name="prob0" value="0.25" />
      <param name="prob1" value="0.5" />
      <param name="prob2" value="0.75" />
      <param name="groupby" value="feature" />
      <param name="featurealphaplot" value="0.05" />
      <param name="featureonlysig" value="TRUE" />
      <output name="adjustedpvalue" file="output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt" compare="sim_size" />
      <output name="iwtomicsrespdf" file="output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf" compare="sim_size" />
      <output name="iwtomicssumpdf" file="output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf" compare="sim_size" />
    </test>
  </tests>

  <help>
This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
for the different tests performed at the selected scale, and it creates a graphical representation of the
Interval-Wise Testing results and a summary plot (optional) at the selected scale.