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comparison loadandplot.xml @ 78:dc2707da8ba4 draft

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Uploaded 20170620
author fabio
date Tue, 20 Jun 2017 13:07:55 -0400
parents 7dcc25a1a062
children 5893ad34d0ac
comparison
equal deleted inserted replaced
77:7bd04a4f29df 78:dc2707da8ba4
13 regionspaths='${region_paths}' 13 regionspaths='${region_paths}'
14 #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] ) 14 #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] )
15 regionsgalaxyids='c(${region_galaxyids})' 15 regionsgalaxyids='c(${region_galaxyids})'
16 #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] ) 16 #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] )
17 regionsfilenames='${region_names}' 17 regionsfilenames='${region_names}'
18 #set region_header = $regionsheadersection.regionsheader 18 #set region_header = $regionsheader
19 #if $region_header != "": 19 #if $region_header != "":
20 regionsheaderfile='${region_header}' 20 regionsheaderfile='${region_header}'
21 #end if 21 #end if
22 22
23 #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] ) 23 #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] )
24 featurespaths='${feature_paths}' 24 featurespaths='${feature_paths}'
25 #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] ) 25 #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] )
26 featuresgalaxyids='c(${feature_galaxyids})' 26 featuresgalaxyids='c(${feature_galaxyids})'
27 #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] ) 27 #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] )
28 featuresfilenames='${feature_names}' 28 featuresfilenames='${feature_names}'
29 #set feature_header = $featuresheadersection.featuresheader 29 #set feature_header = $featuresheader
30 #if $feature_header != "": 30 #if $feature_header != "":
31 featuresheaderfile='${feature_header}' 31 featuresheaderfile='${feature_header}'
32 #end if 32 #end if
33 33
34 smoothing="'${conditionaltype.smoothing}'" 34 smoothing="'${conditionaltype.smoothing}'"
72 </command> 72 </command>
73 73
74 <inputs> 74 <inputs>
75 <!-- regions --> 75 <!-- regions -->
76 <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" /> 76 <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
77 <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."> 77 <param format="tabular" name="regionsheader" type="data" label="Insert header file for regions (optional)" optional="true" 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." />
78 <param format="tabular" name="regionsheader" type="data" label="Select header file" optional="true" />
79 </section>
80 78
81 <!-- features --> 79 <!-- features -->
82 <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" /> 80 <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
83 <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."> 81 <param format="tabular" name="featuresheader" type="data" label="Insert header file for features (optional)" optional="true" 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." />
84 <param format="tabular" name="featuresheader" type="data" label="Select header file" optional="true" />
85 </section>
86 82
87 <!-- zero-base one-base --> 83 <!-- zero-base one-base -->
88 <param name="zerobased" type="select" label="Start positions are:" multiple="false" help=""> 84 <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
89 <option value="TRUE">0-based</option> 85 <option value="TRUE">0-based</option>
90 <option value="FALSE">1-based</option> 86 <option value="FALSE">1-based</option>