Mercurial > repos > fabio > iwtomics
diff testandplot.xml @ 70:39e7294c66e1 draft
Uploaded 20170614
author | fabio |
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date | Wed, 14 Jun 2017 13:57:38 -0400 |
parents | 971bb414cc4f |
children | a3bfaf944f73 |
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--- a/testandplot.xml Fri Jun 09 12:27:10 2017 -0400 +++ b/testandplot.xml Wed Jun 14 13:57:38 2017 -0400 @@ -15,46 +15,46 @@ <command> <![CDATA[ - Rscript $__tool_directory__/testandplot.R adjustedpvaluematrix="${adjustedpvaluematrix}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" iwtomicsrdata="${iwtomicsrdata}" iwtomicstests="${iwtomicstests}" iwtomicsselectedfeatures="${iwtomicsselectedfeatures}" - regionids="${regionids}" - featureids="${featureids}" - rdatafile="${rdata}" + Rscript '$__tool_directory__/testandplot.R' adjustedpvaluematrix='${adjustedpvaluematrix}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' iwtomicsrdata='${iwtomicsrdata}' iwtomicstests='${iwtomicstests}' iwtomicsselectedfeatures='${iwtomicsselectedfeatures}' + regionids='${regionids}' + featureids='${featureids}' + rdatafile='${rdata}' #set region1 = '","'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] ) #set region2 = '","'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] ) - region1="c(${region1})" - region2="c(${region2})" + region1='c(${region1})' + region2='c(${region2})' - features_subset="c(${featureslist})" + features_subset='c(${featureslist})' - statistics="'${conditionalstatistics.statistics}'" + statistics='${conditionalstatistics.statistics}' #if $conditionalstatistics.statistics == "quantile": #set probabilities = '","'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] ) - testprobs="c(${probabilities})" + testprobs='c(${probabilities})' #end if - B="${permutations}" + B='${permutations}' - testalpha="${plotres.alpha}" - average="${plotres.average}" - size="${plotres.size}" - plottype="'${plotres.conditionalplottype.plottype}'" + testalpha='${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},${probs})" + probs='c(${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})" + probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})' #end if #end if - groupby="'${plotsum.conditionalgroupby.groupby}'" + groupby='${plotsum.conditionalgroupby.groupby}' #if $plotsum.conditionalgroupby.groupby == "test": - summaryalpha="${plotsum.conditionalgroupby.testalphaplot}" - only_significant="${plotsum.conditionalgroupby.testonlysig}" + summaryalpha='${plotsum.conditionalgroupby.testalphaplot}' + only_significant='${plotsum.conditionalgroupby.testonlysig}' #elif $plotsum.conditionalgroupby.groupby == "feature": - summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}" - only_significant="${plotsum.conditionalgroupby.featureonlysig}" + summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}' + only_significant='${plotsum.conditionalgroupby.featureonlysig}' #end if >& /dev/null @@ -251,28 +251,6 @@ .. _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> + <expand macro="citations" /> </tool>