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comparison loadandplot.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
equal deleted inserted replaced
71:0c6344d8156b 72:a3bfaf944f73
23 23
24 <command> 24 <command>
25 <![CDATA[ 25 <![CDATA[
26 Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}' 26 Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
27 27
28 #set region_paths = '"\\|"'.join( [ str( $r ) for $r in $regions ] ) 28 #set region_paths = '|'.join( [ str( $r ) for $r in $regions ] )
29 regionspaths='${region_paths}' 29 regionspaths='${region_paths}'
30 #set region_galaxyids = '","'.join( [ str( $r.hid ) for $r in $regions ] ) 30 #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] )
31 regionsgalaxyids='c(${region_galaxyids})' 31 regionsgalaxyids='c(${region_galaxyids})'
32 #set region_names = '"\\|"'.join( [ str( $r.name ) for $r in $regions ] ) 32 #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] )
33 regionsfilenames='${region_names}' 33 regionsfilenames='${region_names}'
34 #set region_header = "${regionsheadersection.regionsheader}" 34 #set region_header = $regionsheadersection.regionsheader
35 #if $region_header != "": 35 #if $region_header != "":
36 regionsheaderfile='${region_header}' 36 regionsheaderfile='${region_header}'
37 #end if 37 #end if
38 38
39 #set feature_paths = '"\\|"'.join( [ str( $f ) for $f in $features ] ) 39 #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] )
40 featurespaths='${feature_paths}' 40 featurespaths='${feature_paths}'
41 #set feature_galaxyids = '","'.join( [ str( $f.hid ) for $f in $features ] ) 41 #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] )
42 featuresgalaxyids='c(${feature_galaxyids})' 42 featuresgalaxyids='c(${feature_galaxyids})'
43 #set feature_names = '"\\|"'.join( [ str( $f.name ) for $f in $features ] ) 43 #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] )
44 featuresfilenames='${feature_names}' 44 featuresfilenames='${feature_names}'
45 #set feature_header = "${featuresheadersection.featuresheader}" 45 #set feature_header = $featuresheadersection.featuresheader
46 #if $feature_header != "": 46 #if $feature_header != "":
47 featuresheaderfile='${feature_header}' 47 featuresheaderfile='${feature_header}'
48 #end if 48 #end if
49 49
50 smoothing='${conditionaltype.smoothing}' 50 smoothing="'${conditionaltype.smoothing}'"
51 start.are.0based='${zerobased}' 51 start.are.0based='${zerobased}'
52 #if $conditionaltype.smoothing == 'no': 52 #if $conditionaltype.smoothing == 'no':
53 alignment='${conditionaltype.alignment}' 53 alignment="'${conditionaltype.alignment}'"
54 #elif $conditionaltype.smoothing == 'locpoly': 54 #elif $conditionaltype.smoothing == 'locpoly':
55 alignment='${conditionaltype.locpolyconditionalscale.alignment}' 55 alignment="'${conditionaltype.locpolyconditionalscale.alignment}'"
56 #if $conditionaltype.locpolyconditionalscale.alignment == 'scale': 56 #if $conditionaltype.locpolyconditionalscale.alignment == 'scale':
57 scale='${conditionaltype.locpolyconditionalscale.scalegrid}' 57 scale='${conditionaltype.locpolyconditionalscale.scalegrid}'
58 #end if 58 #end if
59 bandwidth='${conditionaltype.locpolybandwidth}' 59 bandwidth='${conditionaltype.locpolybandwidth}'
60 degree='${conditionaltype.locpolydegree}' 60 degree='${conditionaltype.locpolydegree}'
61 fill_gaps='${conditionaltype.fillgaps}' 61 fill_gaps='${conditionaltype.fillgaps}'
62 #elif $conditionaltype.smoothing == 'kernel': 62 #elif $conditionaltype.smoothing == 'kernel':
63 alignment='${conditionaltype.kernelconditionalscale.alignment}' 63 alignment="'${conditionaltype.kernelconditionalscale.alignment}'"
64 #if $conditionaltype.kernelconditionalscale.alignment == 'scale': 64 #if $conditionaltype.kernelconditionalscale.alignment == 'scale':
65 scale='${conditionaltype.kernelconditionalscale.scalegrid}' 65 scale='${conditionaltype.kernelconditionalscale.scalegrid}'
66 #end if 66 #end if
67 bandwidth='${conditionaltype.kernelbandwidth}' 67 bandwidth='${conditionaltype.kernelbandwidth}'
68 fill_gaps='${conditionaltype.fillgaps}' 68 fill_gaps='${conditionaltype.fillgaps}'
69 #elif $conditionaltype.smoothing == 'splines': 69 #elif $conditionaltype.smoothing == 'splines':
70 alignment='${conditionaltype.splinesconditionalscale.alignment}' 70 alignment="'${conditionaltype.splinesconditionalscale.alignment}'"
71 #if $conditionaltype.splinesconditionalscale.alignment == 'scale': 71 #if $conditionaltype.splinesconditionalscale.alignment == 'scale':
72 scale='${conditionaltype.splinesconditionalscale.scalegrid}' 72 scale='${conditionaltype.splinesconditionalscale.scalegrid}'
73 #end if 73 #end if
74 degree='${conditionaltype.splinesdegree}' 74 degree='${conditionaltype.splinesdegree}'
75 dist_knots='${conditionaltype.splinesdistknots}' 75 dist_knots='${conditionaltype.splinesdistknots}'
76 fill_gaps='${conditionaltype.fillgaps}' 76 fill_gaps='${conditionaltype.fillgaps}'
77 #end if 77 #end if
78 78
79 average='${plotres.average}' 79 average='${plotres.average}'
80 size='${plotres.size}' 80 size='${plotres.size}'
81 plottype='${plotres.conditionalplottype.plottype}' 81 plottype="'${plotres.conditionalplottype.plottype}'"
82 #if $plotres.conditionalplottype.plottype == 'boxplot': 82 #if $plotres.conditionalplottype.plottype == 'boxplot':
83 #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] ) 83 #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
84 #if $probs != "": 84 #if $probs != "":
85 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})' 85 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
86 #else: 86 #else:
87 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})' 87 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
88 #end if 88 #end if