Mercurial > repos > bgruening > deeptools_compute_matrix

comparison computeMatrix.xml @ 5:345a9a2281e0 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty
author bgruening
date Tue, 22 Dec 2015 13:47:40 -0500
parents 2f2dd609644f
children 451e73bf38fe
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4:28b07293f1ab 5:345a9a2281e0
1 <tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0">
2 <description>preparation step to plot a heatmap or a profile</description> 2 <description>prepares data for plotting a heatmap or a profile of given regions</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">computeMatrix</token> 4 <token name="@BINARY@">computeMatrix</token>
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 tempfile 10 #import tempfile
11 11
12 #for $rf in $regionsFiles:
13 cat "$rf.regionsFile" >> ./temp_input_path;
14 #if str($rf.label.value).strip():
15 echo "\#$rf.label.value" >> ./temp_input_path;
16 #else:
17 echo "\#$rf.regionsFile.name" >> ./temp_input_path;
18 #end if
19 #end for
20
21 @BINARY@ 12 @BINARY@
22 13
23 $mode.mode_select 14 $mode.mode_select
24 --regionsFileName ./temp_input_path 15 --regionsFileName
25 --scoreFileName '$scoreFile' 16 #for $rf in $regionsFiles:
17 '$rf.regionsFile'
18 #end for
19 --scoreFileName
20 #for $bw in $scoreFileName:
21 '$bw'
22 #end for
26 --outFileName '$outFileName' 23 --outFileName '$outFileName'
27 24
28 @THREADS@ 25 @THREADS@
29 26
30 #if $output.showOutputSettings == "yes" 27 #if $output.showOutputSettings == "yes"
31 #if $output.saveData:
32 --outFileNameData '$outFileNameData'
33 #end if
34 #if $output.saveMatrix: 28 #if $output.saveMatrix:
35 --outFileNameMatrix '$outFileNameMatrix' 29 --outFileNameMatrix '$outFileNameMatrix'
36 #end if 30 #end if
37 31
38 #if $output.saveSortedRegions: 32 #if $output.saveSortedRegions:
83 help="File, in BED format, containing the regions to plot."/> 77 help="File, in BED format, containing the regions to plot."/>
84 <param name="label" type="text" size="30" optional="true" value="" label="Label" 78 <param name="label" type="text" size="30" optional="true" value="" label="Label"
85 help="Label to use in the output."/> 79 help="Label to use in the output."/>
86 </repeat> 80 </repeat>
87 81
88 <param name="scoreFile" format="bigwig" type="data" 82 <param name="scoreFileName" format="bigwig" type="data"
89 label="Score file" 83 label="Score file" multiple="True"
90 help="Should be a bigWig file (containing a score, usually covering 84 help="Should be a bigWig file (containing a score, usually covering
91 the whole genome). You can generate a bigWig file either from a 85 the whole genome). You can generate a bigWig file either from a
92 bedGraph or WIG file using UCSC tools or from a BAM file using the 86 bedGraph or WIG file using UCSC tools or from a BAM file using the
93 deepTool bamCoverage. (-scoreFile)"/> 87 deepTool bamCoverage. (--scoreFileName)"/>
94 88
95 <conditional name="mode" > 89 <conditional name="mode" >
96 <param name="mode_select" type="select" 90 <param name="mode_select" type="select"
97 label="computeMatrix has two main output options" 91 label="computeMatrix has two main output options"
98 help="In the scale-regions mode, all regions in the BED file are 92 help="In the scale-regions mode, all regions in the BED file are
212 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> 206 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
213 <expand macro="output_graphic_outputs" /> 207 <expand macro="output_graphic_outputs" />
214 <expand macro="output_save_matrix_values" /> 208 <expand macro="output_save_matrix_values" />
215 </outputs> 209 </outputs>
216 <!-- 210 <!--
217 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 211 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
218 --> 212 -->
219 <tests> 213 <tests>
220 <test> 214 <test>
221 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" /> 215 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
222 <param name="scoreFile" value="bamCoverage_result4.bw" ftype="bigwig" /> 216 <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
223 <param name="showAdvancedOpt" value="yes" /> 217 <param name="showAdvancedOpt" value="yes" />
224 <param name="mode_select" value="reference-point" /> 218 <param name="mode_select" value="reference-point" />
225 <param name="binSize" value="10" /> 219 <param name="binSize" value="10" />
226 <param name="sortUsing" value="sum" /> 220 <param name="sortUsing" value="sum" />
227 <param name="averageTypeBins" value="sum" /> 221 <param name="averageTypeBins" value="sum" />
230 <param name="afterRegionStartLength" value="10" /> 224 <param name="afterRegionStartLength" value="10" />
231 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> 225 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
232 </test> 226 </test>
233 <test> 227 <test>
234 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> 228 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
235 <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" /> 229 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
236 <param name="showAdvancedOpt" value="yes" /> 230 <param name="showAdvancedOpt" value="yes" />
237 <param name="mode_select" value="reference-point" /> 231 <param name="mode_select" value="reference-point" />
238 <param name="binSize" value="10" /> 232 <param name="binSize" value="10" />
239 <param name="beforeRegionStartLength" value="10" /> 233 <param name="beforeRegionStartLength" value="10" />
240 <param name="afterRegionStartLength" value="10" /> 234 <param name="afterRegionStartLength" value="10" />
241 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> 235 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
242 </test> 236 </test>
243 <test> 237 <test>
244 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> 238 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
245 <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" /> 239 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
246 <param name="showAdvancedOpt" value="yes" /> 240 <param name="showAdvancedOpt" value="yes" />
247 <param name="mode_select" value="scale-regions" /> 241 <param name="mode_select" value="scale-regions" />
248 <param name="endLabel" value="END" /> 242 <param name="endLabel" value="END" />
249 <param name="regionStartLength" value="yes" /> 243 <param name="regionStartLength" value="yes" />
250 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> 244 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
269 263
270 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png 264 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
271 :alt: Relationship between computeMatrix, heatmapper and profiler 265 :alt: Relationship between computeMatrix, heatmapper and profiler
272 266
273 267
274 You can find more details on the computeMatrix wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix 268 You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/computeMatrix.html
275 269
276 270
277 ----- 271 -----
278 272
279 @REFERENCES@ 273 @REFERENCES@