Mercurial > repos > fabio > iwtomics
changeset 70:39e7294c66e1 draft
Uploaded 20170614
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--- a/.shed.yml Fri Jun 09 12:27:10 2017 -0400 +++ b/.shed.yml Wed Jun 14 13:57:38 2017 -0400 @@ -1,5 +1,5 @@ name: iwtomics -owner: fabio +owner: iuc categories: - Statistics description: Interval-Wise Testing for Omics Data
--- a/loadandplot.xml Fri Jun 09 12:27:10 2017 -0400 +++ b/loadandplot.xml Wed Jun 14 13:57:38 2017 -0400 @@ -23,68 +23,68 @@ <command> <![CDATA[ - Rscript $__tool_directory__/loadandplot.R outrdata="${outrdata}" outregions="${outregions}" outfeatures="${outfeatures}" outpdf="${outpdf}" + Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}' #set region_paths = '"\\|"'.join( [ str( $r ) for $r in $regions ] ) - regionspaths="${region_paths}" + regionspaths='${region_paths}' #set region_galaxyids = '","'.join( [ str( $r.hid ) for $r in $regions ] ) - regionsgalaxyids="c(${region_galaxyids})" + regionsgalaxyids='c(${region_galaxyids})' #set region_names = '"\\|"'.join( [ str( $r.name ) for $r in $regions ] ) - regionsfilenames="${region_names}" - #set region_header = '"\\|"'.join( [ str( $rh.regionsheader ) for $rh in $regionsheaderrepeat ] ) + regionsfilenames='${region_names}' + #set region_header = "${regionsheadersection.regionsheader}" #if $region_header != "": - regionsheaderfile="${region_header}" + regionsheaderfile='${region_header}' #end if - + #set feature_paths = '"\\|"'.join( [ str( $f ) for $f in $features ] ) - featurespaths="${feature_paths}" + featurespaths='${feature_paths}' #set feature_galaxyids = '","'.join( [ str( $f.hid ) for $f in $features ] ) - featuresgalaxyids="c(${feature_galaxyids})" + featuresgalaxyids='c(${feature_galaxyids})' #set feature_names = '"\\|"'.join( [ str( $f.name ) for $f in $features ] ) - featuresfilenames="${feature_names}" - #set feature_header = '"\\|"'.join( [ str( $fh.featuresheader ) for $fh in $featuresheaderrepeat ] ) + featuresfilenames='${feature_names}' + #set feature_header = "${featuresheadersection.featuresheader}" #if $feature_header != "": - featuresheaderfile="${feature_header}" + featuresheaderfile='${feature_header}' #end if - smoothing="'${conditionaltype.smoothing}'" - start.are.0based="${zerobased}" + smoothing='${conditionaltype.smoothing}' + start.are.0based='${zerobased}' #if $conditionaltype.smoothing == 'no': - alignment="'${conditionaltype.alignment}'" + alignment='${conditionaltype.alignment}' #elif $conditionaltype.smoothing == 'locpoly': - alignment="'${conditionaltype.locpolyconditionalscale.alignment}'" + alignment='${conditionaltype.locpolyconditionalscale.alignment}' #if $conditionaltype.locpolyconditionalscale.alignment == 'scale': - scale="${conditionaltype.locpolyconditionalscale.scalegrid}" + scale='${conditionaltype.locpolyconditionalscale.scalegrid}' #end if - bandwidth="${conditionaltype.locpolybandwidth}" - degree="${conditionaltype.locpolydegree}" - fill_gaps="${conditionaltype.fillgaps}" + bandwidth='${conditionaltype.locpolybandwidth}' + degree='${conditionaltype.locpolydegree}' + fill_gaps='${conditionaltype.fillgaps}' #elif $conditionaltype.smoothing == 'kernel': - alignment="'${conditionaltype.kernelconditionalscale.alignment}'" + alignment='${conditionaltype.kernelconditionalscale.alignment}' #if $conditionaltype.kernelconditionalscale.alignment == 'scale': - scale="${conditionaltype.kernelconditionalscale.scalegrid}" + scale='${conditionaltype.kernelconditionalscale.scalegrid}' #end if - bandwidth="${conditionaltype.kernelbandwidth}" - fill_gaps="${conditionaltype.fillgaps}" + bandwidth='${conditionaltype.kernelbandwidth}' + fill_gaps='${conditionaltype.fillgaps}' #elif $conditionaltype.smoothing == 'splines': - alignment="'${conditionaltype.splinesconditionalscale.alignment}'" + alignment='${conditionaltype.splinesconditionalscale.alignment}' #if $conditionaltype.splinesconditionalscale.alignment == 'scale': - scale="${conditionaltype.splinesconditionalscale.scalegrid}" + scale='${conditionaltype.splinesconditionalscale.scalegrid}' #end if - degree="${conditionaltype.splinesdegree}" - dist_knots="${conditionaltype.splinesdistknots}" - fill_gaps="${conditionaltype.fillgaps}" + degree='${conditionaltype.splinesdegree}' + dist_knots='${conditionaltype.splinesdistknots}' + fill_gaps='${conditionaltype.fillgaps}' #end if - average="${plotres.average}" - size="${plotres.size}" - plottype="'${plotres.conditionalplottype.plottype}'" + 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 @@ -99,15 +99,15 @@ <inputs> <!-- regions --> <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" /> - <repeat name="regionsheaderrepeat" title="Header file for regions (optional)" min="0" max="1" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output."> - <param format="tabular" name="regionsheader" type="data" label="Select header file" /> - </repeat> + <section name="regionsheadersection" title="Insert header file for regions (optional)" expanded="false" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output."> + <param format="tabular" name="regionsheader" type="data" label="Select header file" optional="true" /> + </section> <!-- features --> <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" /> - <repeat name="featuresheaderrepeat" title="Header file for features (optional)" min="0" max="1" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output."> - <param format="tabular" name="featuresheader" type="data" label="Select header file" /> - </repeat> + <section name="featuresheadersection" title="Insert header file for features (optional)" expanded="false" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output."> + <param format="tabular" name="featuresheader" type="data" label="Select header file" optional="true" /> + </section> <!-- zero-base one-base --> <param name="zerobased" type="select" label="Start positions are:" multiple="false" help=""> @@ -330,28 +330,6 @@ .. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example ]]></help> - <citations> - <citation type="bibtex"> - @ARTICLE{ - iwt-functional-data, - author = {Pini, Alessia and Vantini, Simone}, - 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>
--- a/macros.xml Fri Jun 09 12:27:10 2017 -0400 +++ b/macros.xml Wed Jun 14 13:57:38 2017 -0400 @@ -2,8 +2,33 @@ <token name="@VERSION@">1.0.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3.3.1">R</requirement> + <requirement type="package" version="3.3.1">r-base</requirement> <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement> </requirements> </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @ARTICLE{ + iwt-functional-data, + author = {Pini, Alessia and Vantini, Simone}, + 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> + </xml> </macros> \ No newline at end of file
--- a/plotwithscale.xml Fri Jun 09 12:27:10 2017 -0400 +++ b/plotwithscale.xml Wed Jun 14 13:57:38 2017 -0400 @@ -17,38 +17,38 @@ <command> <![CDATA[ - Rscript $__tool_directory__/plotwithscale.R adjustedpvalue="${adjustedpvalue}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" - iwtomicsrdata="${rdata}" - iwtomicstests="${testids}" - iwtomicsselectedfeatures="${featureids}" + Rscript '$__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}" + test_subset='${test_subset}' #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] ) - feature_subset="${feature_subset}" + feature_subset='${feature_subset}' #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] ) - scale_subset="c(${scale_subset})" + scale_subset='c(${scale_subset})' - testalpha="${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 @@ -201,28 +201,6 @@ .. _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>
Binary file test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf has changed
Binary file test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt has changed
--- 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>