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comparison loadandplot.xml @ 70:39e7294c66e1 draft

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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
21 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." /> 21 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
22 </stdio> 22 </stdio>
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 = '"\\|"'.join( [ str( $rh.regionsheader ) for $rh in $regionsheaderrepeat ] ) 34 #set region_header = "${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 = '"\\|"'.join( [ str( $fh.featuresheader ) for $fh in $featuresheaderrepeat ] ) 45 #set feature_header = "${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
89 #end if 89 #end if
90 90
91 >& /dev/null 91 >& /dev/null
92 ]]> 92 ]]>
97 </command> 97 </command>
98 98
99 <inputs> 99 <inputs>
100 <!-- regions --> 100 <!-- regions -->
101 <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" /> 101 <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
102 <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."> 102 <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.">
103 <param format="tabular" name="regionsheader" type="data" label="Select header file" /> 103 <param format="tabular" name="regionsheader" type="data" label="Select header file" optional="true" />
104 </repeat> 104 </section>
105 105
106 <!-- features --> 106 <!-- features -->
107 <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" /> 107 <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
108 <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."> 108 <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.">
109 <param format="tabular" name="featuresheader" type="data" label="Select header file" /> 109 <param format="tabular" name="featuresheader" type="data" label="Select header file" optional="true" />
110 </repeat> 110 </section>
111 111
112 <!-- zero-base one-base --> 112 <!-- zero-base one-base -->
113 <param name="zerobased" type="select" label="Start positions are:" multiple="false" help=""> 113 <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
114 <option value="TRUE">0-based</option> 114 <option value="TRUE">0-based</option>
115 <option value="FALSE">1-based</option> 115 <option value="FALSE">1-based</option>
328 328
329 .. _Simulated_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-example 329 .. _Simulated_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-example
330 .. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example 330 .. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example
331 ]]></help> 331 ]]></help>
332 332
333 <citations> 333 <expand macro="citations" />
334 <citation type="bibtex">
335 @ARTICLE{
336 iwt-functional-data,
337 author = {Pini, Alessia and Vantini, Simone},
338 title = {Interval-Wise Testing for functional data},
339 journal = {Journal of Nonparametric Statistics},
340 year = {2017},
341 volume = {29},
342 number = {2},
343 pages = {407-424}
344 }
345 </citation>
346 <citation type="bibtex">
347 @MANUAL{
348 iwtomics,
349 author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
350 title = {IWTomics: Interval-Wise Testing for Omics Data},
351 note = {R package version 1.0.0},
352 year = {2017}
353 }
354 </citation>
355 </citations>
356 334
357 </tool> 335 </tool>