Mercurial > repos > bgruening > deeptools_compute_matrix

comparison computeMatrix.xml @ 14:5335711251f6 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
author bgruening
date Sun, 14 May 2017 19:20:26 -0400
parents babca70c3586
children 79bc5d836c75
comparison
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13:77c614635e16 14:5335711251f6
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 #import re 10 @multiple_input_bigwigs@
11 #import tempfile
12 #set bw_files=[]
13 #for $counter, $bigwig, in enumerate($scoreFileName):
14 #set identifier = re.sub('[^\s\w\-]', '_', str($bigwig.element_identifier))
15 ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
16 #silent $bw_files.append('%s_%s.bw' % ($identifier, $counter))
17 #end for
18 11
19 #set bed_files=[] 12 #set bed_files=[]
20 #for $counter, $rf, in enumerate($regionsFiles): 13 #for $counter, $rf, in enumerate($regionsFiles):
21 #set identifier = re.sub('[^\s\w\-]', '_', str($rf.regionsFile.element_identifier)) 14 #set identifier = re.sub('[^\s\w\-]', '_', str($rf.regionsFile.element_identifier))
22 ln -f -s "${rf.regionsFile}" "${identifier}_${counter}.bed" && 15 ln -f -s "${rf.regionsFile}" "${identifier}_${counter}.bed" &&
26 @BINARY@ 19 @BINARY@
27 20
28 $mode.mode_select 21 $mode.mode_select
29 --regionsFileName '#echo "' '".join($bed_files)#' 22 --regionsFileName '#echo "' '".join($bed_files)#'
30 23
31 --scoreFileName '#echo "' '".join($bw_files)#' 24 --scoreFileName '#echo "' '".join($files)#'
32 25
33 --outFileName '$outFileName' 26 --outFileName '$outFileName'
34 27
35 @THREADS@ 28 @THREADS@
36 29
77 --maxThreshold $advancedOpt.maxThreshold 70 --maxThreshold $advancedOpt.maxThreshold
78 #end if 71 #end if
79 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': 72 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
80 --scale $advancedOpt.scale 73 --scale $advancedOpt.scale
81 #end if 74 #end if
75 #if $advancedOpt.samplesLabel is not None and str($advancedOpt.samplesLabel) != '':
76 --samplesLabel $advancedOpt.samplesLabel
77 #end if
82 78
83 @ADVANCED_OPTS_GTF@ 79 @ADVANCED_OPTS_GTF@
84 80
85 @blacklist@ 81 @blacklist@
86 82
92 <repeat name="regionsFiles" title="Select regions" min="1"> 88 <repeat name="regionsFiles" title="Select regions" min="1">
93 <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot" 89 <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot"
94 help="File, in BED format, containing the regions to plot."/> 90 help="File, in BED format, containing the regions to plot."/>
95 </repeat> 91 </repeat>
96 92
97 <param name="scoreFileName" format="bigwig" type="data" 93 <expand macro="multiple_input_bigwigs" MIN="1" LABEL="Score file" TITLE="Score files"/>
98 label="Score file" multiple="True"
99 help="You can generate a bigWig file from a BAM file using the
100 bamCoverage tool. (--scoreFileName)"/>
101 94
102 <conditional name="mode" > 95 <conditional name="mode" >
103 <param name="mode_select" type="select" 96 <param name="mode_select" type="select"
104 label="computeMatrix has two main output options" 97 label="computeMatrix has two main output options"
105 help="In the scale-regions mode, all regions in the BED file are 98 help="In the scale-regions mode, all regions in the BED file are
212 numeric value will be skipped. The max threshold is useful to skip those 205 numeric value will be skipped. The max threshold is useful to skip those
213 few regions with very high read counts (e.g. major satellites) that may 206 few regions with very high read counts (e.g. major satellites) that may
214 bias the average values. (--maxThreshold)"/> 207 bias the average values. (--maxThreshold)"/>
215 <param name="scale" type="float" optional="True" label="Scaling factor" 208 <param name="scale" type="float" optional="True" label="Scaling factor"
216 help="If set, all values are multiplied by this number. (--scale)"/> 209 help="If set, all values are multiplied by this number. (--scale)"/>
210 <param argument="--samplesLabel" type="text" size="30"
211 label="Labels for the samples (each bigwig)"
212 help="The default is to use the history item label. The sample labels should be separated by
213 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
214 <sanitizer>
215 <valid initial="string.printable">
216 </valid>
217 </sanitizer>
218 </param>
217 219
218 <expand macro="gtf_options" /> 220 <expand macro="gtf_options" />
219 221
220 <expand macro="blacklist" /> 222 <expand macro="blacklist" />
221 </when> 223 </when>
227 <expand macro="output_save_matrix_values" /> 229 <expand macro="output_save_matrix_values" />
228 </outputs> 230 </outputs>
229 <tests> 231 <tests>
230 <test> 232 <test>
231 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" /> 233 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
232 <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" /> 234 <param name="bigwigfiles" value="bamCoverage_result4.bw" ftype="bigwig" />
233 <param name="showAdvancedOpt" value="yes" /> 235 <param name="showAdvancedOpt" value="yes" />
234 <param name="mode_select" value="reference-point" /> 236 <param name="mode_select" value="reference-point" />
235 <param name="binSize" value="10" /> 237 <param name="binSize" value="10" />
236 <param name="sortUsing" value="sum" /> 238 <param name="sortUsing" value="sum" />
237 <param name="averageTypeBins" value="sum" /> 239 <param name="averageTypeBins" value="sum" />
239 <param name="afterRegionStartLength" value="10" /> 241 <param name="afterRegionStartLength" value="10" />
240 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> 242 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
241 </test> 243 </test>
242 <test> 244 <test>
243 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> 245 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
244 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" /> 246 <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig" />
245 <param name="showAdvancedOpt" value="yes" /> 247 <param name="showAdvancedOpt" value="yes" />
246 <param name="mode_select" value="reference-point" /> 248 <param name="mode_select" value="reference-point" />
247 <param name="binSize" value="10" /> 249 <param name="binSize" value="10" />
248 <param name="beforeRegionStartLength" value="10" /> 250 <param name="beforeRegionStartLength" value="10" />
249 <param name="afterRegionStartLength" value="10" /> 251 <param name="afterRegionStartLength" value="10" />
250 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> 252 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
251 </test> 253 </test>
252 <test> 254 <test>
253 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> 255 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
254 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" /> 256 <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig" />
255 <param name="showAdvancedOpt" value="yes" /> 257 <param name="showAdvancedOpt" value="yes" />
256 <param name="mode_select" value="scale-regions" /> 258 <param name="mode_select" value="scale-regions" />
257 <param name="endLabel" value="END" /> 259 <param name="endLabel" value="END" />
258 <param name="regionStartLength" value="yes" /> 260 <param name="regionStartLength" value="yes" />
259 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> 261 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />