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comparison macros.xml @ 0:fe0243c46b36 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Thu, 30 Mar 2017 02:50:08 -0400
parents
children ef86780a77ff
comparison
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-1:000000000000 0:fe0243c46b36
1 <macros>
2 <xml name="stdio">
3 <stdio>
4 <exit_code range="1:" />
5 <exit_code range=":-1" />
6 <regex match="Error:" />
7 <regex match="Exception:" />
8 <regex match="EXception:" />
9 <regex match="Traceback" />
10 </stdio>
11 </xml>
12
13 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
14 <token name="@WRAPPER_VERSION@">1.7.1</token>
15 <xml name="requirements">
16 <requirements>
17 <requirement type="package" version="2.7.13">python</requirement>
18 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
19 <yield />
20 </requirements>
21 <expand macro="stdio" />
22 <version_command>@BINARY@ --version</version_command>
23 </xml>
24
25 <xml name="citations">
26 <citations>
27 <citation type="doi">10.5281/zenodo.159780</citation>
28 <yield />
29 </citations>
30 </xml>
31
32 <xml name="zMax">
33 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
34 </xml>
35
36 <xml name="colormap">
37 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
38 <option value="RdYlBu">RdYlBu</option>
39 <option value="Accent">Accent</option>
40 <option value="Spectral">Spectral</option>
41 <option value="Set1">Set1</option>
42 <option value="Set2">Set2</option>
43 <option value="Set3">Set3</option>
44 <option value="Dark2">Dark2</option>
45 <option value="Reds">Reds</option>
46 <option value="Oranges">Oranges</option>
47 <option value="Greens">Greens</option>
48 <option value="Blues">Blues</option>
49 <option value="Greys">Greys</option>
50 <option value="Purples">Purples</option>
51 <option value="Paired">Paired</option>
52 <option value="Pastel1">Pastel1</option>
53 <option value="Pastel2">Pastel2</option>
54 <option value="spring">spring</option>
55 <option value="summer">summer</option>
56 <option value="autumn">autumn</option>
57 <option value="winter">winter</option>
58 <option value="hot">hot</option>
59 <option value="coolwarm">coolwarm</option>
60 <option value="cool">cool</option>
61 <option value="seismic">seismic</option>
62 <option value="terrain">terrain</option>
63 <option value="ocean">ocean</option>
64 <option value="rainbow">rainbow</option>
65 <option value="bone">bone</option>
66 <option value="flag">flag</option>
67 <option value="prism">prism</option>
68 <option value="cubehelix">cubehelix</option>
69 <option value="binary">binary</option>
70 <option value="pink">pink</option>
71 <option value="gray">gray</option>
72 <option value="copper">copper</option>
73 <option value="BrBG">BrBG</option>
74 <option value="BuGn">BuGn</option>
75 <option value="BuPu">BuPu</option>
76 <option value="GnBu">GnBu</option>
77 <option value="OrRd">OrRd</option>
78 <option value="PiYG">PiYG</option>
79 <option value="PRGn">PRGn</option>
80 <option value="PuOr">PuOr</option>
81 <option value="PuRd">PuRd</option>
82 <option value="PuBu">PuBu</option>
83 <option value="RdBu">RdBu</option>
84 <option value="RdGy">RdGy</option>
85 <option value="RdPu">RdPu</option>
86 <option value="YlGn">YlGn</option>
87 <option value="PuBuGn">PuBuGn</option>
88 <option value="RdYlGn">RdYlGn</option>
89 <option value="YlGnBu">YlGnBu</option>
90 <option value="YlOrBr">YlOrBr</option>
91 <option value="YlOrRd">YlOrRd</option>
92 <option value="gist_gray">gist_gray</option>
93 <option value="gist_stern">gist_stern</option>
94 <option value="gist_earth">gist_earth</option>
95 <option value="gist_yarg">gist_yarg</option>
96 <option value="gist_ncar">gist_ncar</option>
97 <option value="gist_rainbow">gist_rainbow</option>
98 <option value="gist_heat">gist_heat</option>
99 <option value="gnuplot">gnuplot</option>
100 <option value="gnuplot2">gnuplot2</option>
101 <option value="CMRmap">CMRmap</option>
102 <option value="bwr">bwr</option>
103 <option value="hsv">hsv</option>
104 <option value="brg">brg</option>
105 <option value="jet">jet</option>
106 <option value="afmhot">afmhot</option>
107 <option value="Accent_r">Accent reversed</option>
108 <option value="Spectral_r">Spectral reversed</option>
109 <option value="Set1_r">Set1 reversed</option>
110 <option value="Set2_r">Set2 reversed</option>
111 <option value="Set3_r">Set3 reversed</option>
112 <option value="Dark2_r">Dark2 reversed</option>
113 <option value="Reds_r">Reds reversed</option>
114 <option value="Oranges_r">Oranges reversed</option>
115 <option value="Greens_r">Greens reversed</option>
116 <option value="Blues_r">Blues reversed</option>
117 <option value="Greys_r">Greys reversed</option>
118 <option value="Purples_r">Purples reversed</option>
119 <option value="Paired_r">Paired reversed</option>
120 <option value="Pastel1_r">Pastel1 reversed</option>
121 <option value="Pastel2_r">Pastel2 reversed</option>
122 <option value="spring_r">spring reversed</option>
123 <option value="summer_r">summer reversed</option>
124 <option value="autumn_r">autumn reversed</option>
125 <option value="winter_r">winter reversed</option>
126 <option value="hot_r">hot reversed</option>
127 <option value="coolwarm_r">coolwarm reversed</option>
128 <option value="cool_r">cool reversed</option>
129 <option value="seismic_r">seismic reversed</option>
130 <option value="terrain_r">terrain reversed</option>
131 <option value="ocean_r">ocean reversed</option>
132 <option value="rainbow_r">rainbow reversed</option>
133 <option value="bone_r">bone reversed</option>
134 <option value="flag_r">flag reversed</option>
135 <option value="prism_r">prism reversed</option>
136 <option value="cubehelix_r">cubehelix reversed</option>
137 <option value="binary_r">binary reversed</option>
138 <option value="pink_r">pink reversed</option>
139 <option value="gray_r">gray reversed</option>
140 <option value="copper_r">copper reversed</option>
141 <option value="BrBG_r">BrBG reversed</option>
142 <option value="BuGn_r">BuGn reversed</option>
143 <option value="BuPu_r">BuPu reversed</option>
144 <option value="GnBu_r">GnBu reversed</option>
145 <option value="OrRd_r">OrRd reversed</option>
146 <option value="PiYG_r">PiYG reversed</option>
147 <option value="PRGn_r">PRGn reversed</option>
148 <option value="PuOr_r">PuOr reversed</option>
149 <option value="PuRd_r">PuRd reversed</option>
150 <option value="PuBu_r">PuBu reversed</option>
151 <option value="RdBu_r">RdBu reversed</option>
152 <option value="RdGy_r">RdGy reversed</option>
153 <option value="RdPu_r">RdPu reversed</option>
154 <option value="YlGn_r">YlGn reversed</option>
155 <option value="PuBuGn_r">PuBuGn reversed</option>
156 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
157 <option value="RdYlGn_r">RdYlGn reversed</option>
158 <option value="YlGnBu_r">YlGnBu reversed</option>
159 <option value="YlOrBr_r">YlOrBr reversed</option>
160 <option value="YlOrRd_r">YlOrRd reversed</option>
161 <option value="gist_gray_r">gist_gray reversed</option>
162 <option value="gist_stern_r">gist_stern reversed</option>
163 <option value="gist_earth_r">gist_earth reversed</option>
164 <option value="gist_yarg_r">gist_yarg reversed</option>
165 <option value="gist_ncar_r">gist_ncar reversed</option>
166 <option value="gist_rainbow_r">gist_rainbow reversed</option>
167 <option value="gist_heat_r">gist_heat reversed</option>
168 <option value="gnuplot_r">gnuplot reversed</option>
169 <option value="gnuplot2_r">gnuplot2 reversed</option>
170 <option value="CMRmap_r">CMRmap reversed</option>
171 <option value="bwr_r">bwr reversed</option>
172 <option value="hsv_r">hsv reversed</option>
173 <option value="brg_r">brg reversed</option>
174 <option value="jet_r">jet reversed</option>
175 <option value="afmhot_r">afmhot reversed</option>
176 </param>
177 </xml>
178
179
180 <xml name="multiple_input_matrices">
181 <repeat name="input_files" title="HiC Matrix files" min="2">
182 <param name="matrix" type="data" format="h5"
183 label="HiC Matrix file"
184 help=""/>
185 <param name="mlabel" type="text" size="30" optional="true" value=""
186 label="Label"
187 help="Label to use in the output. If not given the dataset name will be used instead."/>
188 </repeat>
189 </xml>
190
191 <token name="@multiple_input_matrices@">
192 #set $matrices = []
193 #set $mlabels = []
194 #for $counter, $i in enumerate($input_files):
195 ln -s $i.matrix #echo str($counter)+'.npz.h5'#;
196 #silent $matrices.append( '%s.npz.h5' % $counter )
197
198 #if str($i.mlabel.value) != "":
199 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
200 #else
201 #set $mlabels += ['"%s"' % ($i.matrix.name)]
202 #end if
203 #end for
204 #set $mlabels = ' '.join($mlabels)
205 #set $matrices = ' '.join($matrices)
206 </token>
207
208
209 <xml name="region">
210 <param name="region" type="text" label="Region of the genome to limit the operation"
211 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
212 </xml>
213
214
215
216 <xml name="kmeans_clustering">
217 <conditional name="used_multiple_regions">
218 <param name="used_multiple_regions_options" type="select"
219 label="Did you compute the matrix with more than one groups of regions?"
220 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
221 <option value="yes">Yes, I used multiple groups of regions</option>
222 <option value="no">No, I used only one group</option>
223 </param>
224 <when value="no">
225 <conditional name="clustering">
226 <param name="clustering_options" type="select" label="Clustering algorithm">
227 <option value="none">No clustering</option>
228 <option value="kmeans">Kmeans clustering</option>
229 </param>
230 <when value="kmeans">
231 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
232 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
233 </when>
234 <when value="none" />
235 </conditional>
236 </when>
237 <when value="yes" />
238 </conditional>
239 </xml>
240
241 <token name="@KMEANS_CLUSTERING@">
242 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
243 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
244 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
245 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
246 #end if
247 #end if
248 #end if
249 </token>
250
251 <xml name="samFlag">
252 <param name="samFlag" type="integer" optional="true" value=""
253 label="Filter reads based on the SAM flag"
254 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
255 </xml>
256 <xml name="plotNumbers">
257 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
258 label="Plot the correlation value"
259 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
260 </xml>
261 <xml name="doNotExtendPairedEnds">
262 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
263 label="Do not extend paired ends"
264 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
265 </xml>
266
267 <xml name="ignoreDuplicates">
268 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
269 label="Ignore duplicates"
270 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
271 </xml>
272
273 <xml name="minMappingQuality">
274 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
275 label="Minimum mapping quality"
276 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
277 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
278 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
279 </xml>
280
281 <xml name="skipZeros">
282 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
283 label ="Skip zeros"
284 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
285 </xml>
286
287 <xml name="fragmentLength">
288 <param name="fragmentLength" type="integer" value="300" min="1"
289 label="Fragment length used for the sequencing"
290 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
291 </xml>
292
293 <xml name="scaleFactor">
294 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
295 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
296 </xml>
297
298 <xml name="xMax">
299 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
300 label="Max value for the x-axis in counts per bin" />
301 </xml>
302
303 <xml name="filterThreshold">
304 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
305 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
306
307 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
308 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
309 </xml>
310
311
312 <xml name="pseudocount">
313 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
314 </xml>
315
316 <token name="@REFERENCES@">
317
318 .. class:: infomark
319
320 For more information on the tools, please visit our `help site`_.
321
322 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
323
324 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
325
326 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
327 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
328 .. _help site: https://github.com/fidelram/deepTools/wiki/
329
330 </token>
331
332
333 <xml name="multiple_input_bams">
334 <repeat name="input_files" title="BAM files" min="2">
335 <param name="bamfile" type="data" format="bam"
336 label="Bam file"
337 help="The BAM file must be sorted."/>
338 <param name="label" type="text" size="30" optional="true" value=""
339 label="Label"
340 help="Label to use in the output. If not given the dataset name will be used instead."/>
341 </repeat>
342 </xml>
343
344 <xml name="multiple_input_bigwigs">
345 <repeat name="input_files" title="BigWig files" min="2">
346 <param name="bigwigfile" type="data" format="bigwig"
347 label="Bigwig file"
348 help="The Bigwig file must be sorted."/>
349 <param name="label" type="text" size="30" optional="true" value=""
350 label="Label"
351 help="Label to use in the output. If not given the dataset name will be used instead."/>
352 </repeat>
353 </xml>
354
355 <xml name="plotTitle">
356 <param name="plotTitle" type="text" value="" size="30" optional="True"
357 label="Title of the plot"
358 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
359 </xml>
360
361 <token name="@multiple_input_bams@">
362 #import tempfile
363 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
364 #set files=[]
365 #set labels=[]
366 #for $i in $input_files:
367 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
368 #set $temp_input_path = $temp_input_handle.name
369 #silent $temp_input_handle.close()
370 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
371 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
372 #silent $files.append('%s.bam' % $temp_input_path)
373
374 ##set $files += [str($i.bamfile)]
375 #if str($i.label.value) != "":
376 #set $labels += ["\"%s\"" % ($i.label.value)]
377 #else
378 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
379 #end if
380 #end for
381 </token>
382
383 <token name="@multiple_input_bigwigs@">
384 #import tempfile
385 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
386 #set files=[]
387 #set labels=[]
388 #for $i in $input_files:
389 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
390 #set $temp_input_path = $temp_input_handle.name
391 #silent $temp_input_handle.close()
392 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
393 #silent $files.append('%s.bw' % $temp_input_path)
394
395 ##set $files += [str($i.bigwigfile)]
396 #if str($i.label.value) != "":
397 #set $labels += ["\"%s\"" % ($i.label.value)]
398 #else
399 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
400 #end if
401 #end for
402 </token>
403
404 <xml name="reference_genome_source">
405 <conditional name="source">
406 <param name="ref_source" type="select" label="Reference genome">
407 <option value="cached">locally cached</option>
408 <option value="history">in your history</option>
409 </param>
410 <when value="cached">
411 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
412 <options from_data_table="deepTools_seqs">
413 <filter type="sort_by" column="1" />
414 <validator type="no_options" message="No indexes are available." />
415 </options>
416 </param>
417 </when>
418 <when value="history">
419 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
420 </when>
421 </conditional>
422 </xml>
423
424 <token name="@reference_genome_source@">
425 #if $source.ref_source=="history":
426 --genome $source.input1
427 #else:
428 --genome "${source.input1_2bit.fields.path}"
429 #end if
430 </token>
431
432 <xml name="effectiveGenomeSize">
433 <conditional name="effectiveGenomeSize">
434 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
435 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
436 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
437 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
438 <option value="93260000">ce10 (93260000)</option>
439 <option value="121400000">dm3 (121400000)</option>
440 <option value="2451960000" selected="true">hg19 (2451960000)</option>
441 <option value="2150570000">mm9 (2150570000)</option>
442 <option value="specific">user specified</option>
443 </param>
444 <when value="specific">
445 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
446 </when>
447 <when value="2150570000" />
448 <when value="2451960000" />
449 <when value="121400000" />
450 <when value="93260000" />
451 </conditional>
452 </xml>
453
454 <xml name="image_file_format">
455 <param name="outFileFormat" type="select" label="Image file format">
456 <option value="png" selected="true">png</option>
457 <option value="pdf">pdf</option>
458 <option value="svg">svg</option>
459 <option value="eps">eps</option>
460 <option value="emf">emf</option>
461 </param>
462 </xml>
463
464 <xml name="missingDataAsZero">
465 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
466 label ="Treat missing data as zero"
467 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
468 </xml>
469
470 <xml name="input_save_matrix_values">
471 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
472 </xml>
473
474 <xml name="input_graphic_output_settings">
475 <conditional name="output" >
476 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
477 <option value="no" selected="true">no</option>
478 <option value="yes">yes</option>
479 </param>
480 <when value="no" />
481 <when value="yes">
482 <yield />
483 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
484 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
485 </when>
486 </conditional>
487 </xml>
488
489 <xml name="input_image_file_format">
490 <param name="outFileFormat" type="select" label="Image file format">
491 <option value="png" selected="true">png</option>
492 <option value="pdf">pdf</option>
493 <option value="svg">svg</option>
494 <option value="eps">eps</option>
495 <option value="emf">emf</option>
496 </param>
497 </xml>
498
499 <xml name="output_image_file_format">
500 <data format="png" name="outFileName" label="${tool.name} image">
501 <change_format>
502 <when input="output.outFileFormat" value="pdf" format="pdf" />
503 <when input="output.outFileFormat" value="svg" format="svg" />
504 <when input="output.outFileFormat" value="eps" format="eps" />
505 <when input="output.outFileFormat" value="emf" format="emf" />
506 </change_format>
507 </data>
508 </xml>
509
510 <xml name="output_save_matrix_values">
511 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
512 <filter>
513 ((
514 output['showOutputSettings'] == 'yes' and
515 output['saveMatrix'] is True
516 ))
517 </filter>
518 </data>
519 </xml>
520
521 <xml name="output_graphic_outputs">
522 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
523 <filter>
524 ((
525 output['showOutputSettings'] == 'yes' and
526 output['saveData'] is True
527 ))
528 </filter>
529 </data>
530 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
531 <filter>
532 ((
533 output['showOutputSettings'] == 'yes' and
534 output['saveSortedRegions'] is True
535 ))
536 </filter>
537 </data>
538 </xml>
539
540
541
542 </macros>