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comparison computeMatrix.xml @ 6:451e73bf38fe draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41
author bgruening
date Wed, 23 Dec 2015 04:00:26 -0500
parents 345a9a2281e0
children 021729469baf
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5:345a9a2281e0 6:451e73bf38fe
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>prepares data for plotting a heatmap or a profile of given regions</description> 2 <description>preparation step to plot a heatmap or a profile</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
12 @BINARY@ 21 @BINARY@
13 22
14 $mode.mode_select 23 $mode.mode_select
15 --regionsFileName 24 --regionsFileName ./temp_input_path
16 #for $rf in $regionsFiles: 25 --scoreFileName '$scoreFile'
17 '$rf.regionsFile'
18 #end for
19 --scoreFileName
20 #for $bw in $scoreFileName:
21 '$bw'
22 #end for
23 --outFileName '$outFileName' 26 --outFileName '$outFileName'
24 27
25 @THREADS@ 28 @THREADS@
26 29
27 #if $output.showOutputSettings == "yes" 30 #if $output.showOutputSettings == "yes"
31 #if $output.saveData:
32 --outFileNameData '$outFileNameData'
33 #end if
28 #if $output.saveMatrix: 34 #if $output.saveMatrix:
29 --outFileNameMatrix '$outFileNameMatrix' 35 --outFileNameMatrix '$outFileNameMatrix'
30 #end if 36 #end if
31 37
32 #if $output.saveSortedRegions: 38 #if $output.saveSortedRegions:
77 help="File, in BED format, containing the regions to plot."/> 83 help="File, in BED format, containing the regions to plot."/>
78 <param name="label" type="text" size="30" optional="true" value="" label="Label" 84 <param name="label" type="text" size="30" optional="true" value="" label="Label"
79 help="Label to use in the output."/> 85 help="Label to use in the output."/>
80 </repeat> 86 </repeat>
81 87
82 <param name="scoreFileName" format="bigwig" type="data" 88 <param name="scoreFile" format="bigwig" type="data"
83 label="Score file" multiple="True" 89 label="Score file"
84 help="Should be a bigWig file (containing a score, usually covering 90 help="Should be a bigWig file (containing a score, usually covering
85 the whole genome). You can generate a bigWig file either from a 91 the whole genome). You can generate a bigWig file either from a
86 bedGraph or WIG file using UCSC tools or from a BAM file using the 92 bedGraph or WIG file using UCSC tools or from a BAM file using the
87 deepTool bamCoverage. (--scoreFileName)"/> 93 deepTool bamCoverage. (-scoreFile)"/>
88 94
89 <conditional name="mode" > 95 <conditional name="mode" >
90 <param name="mode_select" type="select" 96 <param name="mode_select" type="select"
91 label="computeMatrix has two main output options" 97 label="computeMatrix has two main output options"
92 help="In the scale-regions mode, all regions in the BED file are 98 help="In the scale-regions mode, all regions in the BED file are
206 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> 212 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
207 <expand macro="output_graphic_outputs" /> 213 <expand macro="output_graphic_outputs" />
208 <expand macro="output_save_matrix_values" /> 214 <expand macro="output_save_matrix_values" />
209 </outputs> 215 </outputs>
210 <!-- 216 <!--
211 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 217 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
212 --> 218 -->
213 <tests> 219 <tests>
214 <test> 220 <test>
215 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" /> 221 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
216 <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" /> 222 <param name="scoreFile" value="bamCoverage_result4.bw" ftype="bigwig" />
217 <param name="showAdvancedOpt" value="yes" /> 223 <param name="showAdvancedOpt" value="yes" />
218 <param name="mode_select" value="reference-point" /> 224 <param name="mode_select" value="reference-point" />
219 <param name="binSize" value="10" /> 225 <param name="binSize" value="10" />
220 <param name="sortUsing" value="sum" /> 226 <param name="sortUsing" value="sum" />
221 <param name="averageTypeBins" value="sum" /> 227 <param name="averageTypeBins" value="sum" />
224 <param name="afterRegionStartLength" value="10" /> 230 <param name="afterRegionStartLength" value="10" />
225 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> 231 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
226 </test> 232 </test>
227 <test> 233 <test>
228 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> 234 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
229 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" /> 235 <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
230 <param name="showAdvancedOpt" value="yes" /> 236 <param name="showAdvancedOpt" value="yes" />
231 <param name="mode_select" value="reference-point" /> 237 <param name="mode_select" value="reference-point" />
232 <param name="binSize" value="10" /> 238 <param name="binSize" value="10" />
233 <param name="beforeRegionStartLength" value="10" /> 239 <param name="beforeRegionStartLength" value="10" />
234 <param name="afterRegionStartLength" value="10" /> 240 <param name="afterRegionStartLength" value="10" />
235 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> 241 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
236 </test> 242 </test>
237 <test> 243 <test>
238 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> 244 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
239 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" /> 245 <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
240 <param name="showAdvancedOpt" value="yes" /> 246 <param name="showAdvancedOpt" value="yes" />
241 <param name="mode_select" value="scale-regions" /> 247 <param name="mode_select" value="scale-regions" />
242 <param name="endLabel" value="END" /> 248 <param name="endLabel" value="END" />
243 <param name="regionStartLength" value="yes" /> 249 <param name="regionStartLength" value="yes" />
244 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> 250 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
263 269
264 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png 270 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
265 :alt: Relationship between computeMatrix, heatmapper and profiler 271 :alt: Relationship between computeMatrix, heatmapper and profiler
266 272
267 273
268 You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/computeMatrix.html 274 You can find more details on the computeMatrix wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix
269 275
270 276
271 ----- 277 -----
272 278
273 @REFERENCES@ 279 @REFERENCES@