kt_summarize.xml

<tool id="kt_summarize" name="ktoolu summarize" version="0.1.0">
    <description>Summarize and visualize kraken classification results</description>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
        <requirement type="package">krona</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command interpreter="python"><![CDATA[
        kt_summarize.py
        #if $includeUnclassifiedReads == "includeUnclassifiedYes":
          --include-unclassified
        #end if
        #if $drawKronaPlot == "drawKronaPlotYes":
          --draw-krona-plot "${kronaPlot}"
        #end if
        #if $writeSummary == "writeSummaryYes":
          --write-summary "${summaryTable}"
        #end if
         "${kraken_results}"
    ]]></command>
    <inputs>
      <param name="kraken_results" type="data" format="tabular" label="Kraken classification output" />
      <param name="drawKronaPlot" type="select" label="Draw Krona plot?">
        <option value="drawKronaPlotYes">Yes</option>
        <option value="drawKronaPlotNo">No</option>
      </param>
      <param name="writeSummary" type="select" label="Write summary table?">
        <option value="writeSummaryYes">Yes</option>
        <option value="writeSummaryNo">No</option>
      </param>
      <param name="includeUnclassifiedReads" type="select" label="Include unclassified reads?">
        <option value="includeUnclassifiedNo">No</option>
        <option value="includeUnclassifiedYes">Yes</option>
      </param>
    </inputs>
    <outputs>
      <data format="html" name="kronaPlot" label="Krona visualization of ${tool.name}">
        <filter>drawKronaPlot == "drawKronaPlotYes"</filter>
      </data>
      <data format="tabular" name="summaryTable" label="${tool.name} summary table">
        <filter>writeSummary == "writeSummaryYes"</filter>
      </data>


    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>