Mercurial > repos > fabio > iwtomics
comparison testandplot.xml @ 72:a3bfaf944f73 draft
Uploaded 20170614
author | fabio |
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date | Wed, 14 Jun 2017 15:20:32 -0400 |
parents | 39e7294c66e1 |
children | 2bb6b44093ba |
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71:0c6344d8156b | 72:a3bfaf944f73 |
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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}' |