Mercurial > repos > fabio > iwtomics

comparison testandplot.xml @ 70:39e7294c66e1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded 20170614
author fabio
date Wed, 14 Jun 2017 13:57:38 -0400
parents 971bb414cc4f
children a3bfaf944f73
comparison
equal deleted inserted replaced
69:4935e8a8f0b1 70:39e7294c66e1
13 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." /> 13 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
14 </stdio> 14 </stdio>
15 15
16 <command> 16 <command>
17 <![CDATA[ 17 <![CDATA[
18 Rscript $__tool_directory__/testandplot.R adjustedpvaluematrix="${adjustedpvaluematrix}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" iwtomicsrdata="${iwtomicsrdata}" iwtomicstests="${iwtomicstests}" iwtomicsselectedfeatures="${iwtomicsselectedfeatures}" 18 Rscript '$__tool_directory__/testandplot.R' adjustedpvaluematrix='${adjustedpvaluematrix}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' iwtomicsrdata='${iwtomicsrdata}' iwtomicstests='${iwtomicstests}' iwtomicsselectedfeatures='${iwtomicsselectedfeatures}'
19 regionids="${regionids}" 19 regionids='${regionids}'
20 featureids="${featureids}" 20 featureids='${featureids}'
21 rdatafile="${rdata}" 21 rdatafile='${rdata}'
22 22
23 #set region1 = '","'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] ) 23 #set region1 = '","'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
24 #set region2 = '","'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] ) 24 #set region2 = '","'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
25 region1="c(${region1})" 25 region1='c(${region1})'
26 region2="c(${region2})" 26 region2='c(${region2})'
27 27
28 features_subset="c(${featureslist})" 28 features_subset='c(${featureslist})'
29 29
30 statistics="'${conditionalstatistics.statistics}'" 30 statistics='${conditionalstatistics.statistics}'
31 #if $conditionalstatistics.statistics == "quantile": 31 #if $conditionalstatistics.statistics == "quantile":
32 #set probabilities = '","'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] ) 32 #set probabilities = '","'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
33 testprobs="c(${probabilities})" 33 testprobs='c(${probabilities})'
34 #end if 34 #end if
35 35
36 B="${permutations}" 36 B='${permutations}'
37 37
38 testalpha="${plotres.alpha}" 38 testalpha='${plotres.alpha}'
39 average="${plotres.average}" 39 average='${plotres.average}'
40 size="${plotres.size}" 40 size='${plotres.size}'
41 plottype="'${plotres.conditionalplottype.plottype}'" 41 plottype='${plotres.conditionalplottype.plottype}'
42 #if $plotres.conditionalplottype.plottype == 'boxplot': 42 #if $plotres.conditionalplottype.plottype == 'boxplot':
43 #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] ) 43 #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
44 #if $probs != "": 44 #if $probs != "":
45 probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})" 45 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
46 #else: 46 #else:
47 probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})" 47 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
48 #end if 48 #end if
49 #end if 49 #end if
50 50
51 groupby="'${plotsum.conditionalgroupby.groupby}'" 51 groupby='${plotsum.conditionalgroupby.groupby}'
52 #if $plotsum.conditionalgroupby.groupby == "test": 52 #if $plotsum.conditionalgroupby.groupby == "test":
53 summaryalpha="${plotsum.conditionalgroupby.testalphaplot}" 53 summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
54 only_significant="${plotsum.conditionalgroupby.testonlysig}" 54 only_significant='${plotsum.conditionalgroupby.testonlysig}'
55 #elif $plotsum.conditionalgroupby.groupby == "feature": 55 #elif $plotsum.conditionalgroupby.groupby == "feature":
56 summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}" 56 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
57 only_significant="${plotsum.conditionalgroupby.featureonlysig}" 57 only_significant='${plotsum.conditionalgroupby.featureonlysig}'
58 #end if 58 #end if
59 59
60 >& /dev/null 60 >& /dev/null
61 ]]> 61 ]]>
62 <!-- 62 <!--
249 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_). 249 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
250 250
251 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf 251 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
252 ]]></help> 252 ]]></help>
253 253
254 <citations> 254 <expand macro="citations" />
255 <citation type="bibtex">
256 @ARTICLE{
257 iwt-functional-data,
258 author = {A Pini and S. Vantini},
259 title = {Interval-Wise Testing for functional data},
260 journal = {Journal of Nonparametric Statistics},
261 year = {2017},
262 volume = {29},
263 number = {2},
264 pages = {407-424}
265 }
266 </citation>
267 <citation type="bibtex">
268 @MANUAL{
269 iwtomics,
270 author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
271 title = {IWTomics: Interval-Wise Testing for Omics Data},
272 note = {R package version 1.0.0},
273 year = {2017}
274 }
275 </citation>
276 </citations>
277 255
278 </tool> 256 </tool>