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comparison testandplot.xml @ 72:a3bfaf944f73 draft

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Uploaded 20170614
author fabio
date Wed, 14 Jun 2017 15:20:32 -0400
parents 39e7294c66e1
children 2bb6b44093ba
comparison
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71:0c6344d8156b 72:a3bfaf944f73
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}'