Mercurial > repos > bgruening > deeptools_compute_matrix
comparison computeMatrix.xml @ 14:5335711251f6 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
author | bgruening |
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date | Sun, 14 May 2017 19:20:26 -0400 |
parents | babca70c3586 |
children | 79bc5d836c75 |
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13:77c614635e16 | 14:5335711251f6 |
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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 "label 2""> | |
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" /> |