comparison plotwithscale.xml @ 70:39e7294c66e1 draft

Uploaded 20170614

69:4935e8a8f0b1

    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
  </stdio>

  <command>
<![CDATA[
    Rscript $__tool_directory__/plotwithscale.R adjustedpvalue="${adjustedpvalue}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}"
      iwtomicsrdata="${rdata}"
      iwtomicstests="${testids}"
      iwtomicsselectedfeatures="${featureids}"

      #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
      test_subset="${test_subset}"
      #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
      feature_subset="${feature_subset}"
      #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
      scale_subset="c(${scale_subset})"

      testalpha="${plotres.alpha}"
      average="${plotres.average}"
      size="${plotres.size}"
      plottype="'${plotres.conditionalplottype.plottype}'"
      #if $plotres.conditionalplottype.plottype == 'boxplot':
        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
        #if $probs != "":
          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"
        #else:
          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"
        #end if
      #end if

      groupby="'${plotsum.conditionalgroupby.groupby}'"
      #if $plotsum.conditionalgroupby.groupby == "test":
        summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"
        only_significant="${plotsum.conditionalgroupby.testonlysig}"
      #elif $plotsum.conditionalgroupby.groupby == "feature":
        summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"
        only_significant="${plotsum.conditionalgroupby.featureonlysig}"
      #end if

      >& /dev/null
]]>
    <!--

The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).

.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
  ]]></help>

  <citations>
    <citation type="bibtex">
      @ARTICLE{
               iwt-functional-data,
               author = {A Pini and S. Vantini},
               title = {Interval-Wise Testing for functional data},
               journal = {Journal of Nonparametric Statistics},
               year = {2017},
               volume = {29},
               number = {2},
               pages = {407-424}
      }
    </citation>
    <citation type="bibtex">
      @MANUAL{
               iwtomics,
               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
               title = {IWTomics: Interval-Wise Testing for Omics Data},
               note = {R package version 1.0.0},
               year = {2017}
      }
    </citation>
  </citations>

</tool>

70:39e7294c66e1

    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
  </stdio>

  <command>
<![CDATA[
    Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
      iwtomicsrdata='${rdata}'
      iwtomicstests='${testids}'
      iwtomicsselectedfeatures='${featureids}'

      #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
      test_subset='${test_subset}'
      #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
      feature_subset='${feature_subset}'
      #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
      scale_subset='c(${scale_subset})'

      testalpha='${plotres.alpha}'
      average='${plotres.average}'
      size='${plotres.size}'
      plottype='${plotres.conditionalplottype.plottype}'
      #if $plotres.conditionalplottype.plottype == 'boxplot':
        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
        #if $probs != "":
          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
        #else:
          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
        #end if
      #end if

      groupby='${plotsum.conditionalgroupby.groupby}'
      #if $plotsum.conditionalgroupby.groupby == "test":
        summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
        only_significant='${plotsum.conditionalgroupby.testonlysig}'
      #elif $plotsum.conditionalgroupby.groupby == "feature":
        summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
        only_significant='${plotsum.conditionalgroupby.featureonlysig}'
      #end if

      >& /dev/null
]]>
    <!--

The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).

.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
  ]]></help>

  <expand macro="citations" />

</tool>