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comparison macros.xml @ 0:58d146c74d72 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:11:56 -0500
parents
children eec0210589b3
comparison
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-1:000000000000 0:58d146c74d72
1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <token name="@WRAPPER_VERSION@">2.0</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
7 <yield />
8 </requirements>
9 <version_command>@BINARY@ --version</version_command>
10 </xml>
11
12 <xml name="citations">
13 <citations>
14 <citation type="doi">10.5281/zenodo.1123667</citation>
15 <yield />
16 </citations>
17 </xml>
18
19 <xml name="zMax">
20 <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 -->
21 </xml>
22
23 <xml name="colormap">
24 <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: https://matplotlib.org/examples/color/colormaps_reference.html">
25 <option value="RdYlBu">RdYlBu</option>
26 <option value="Accent">Accent</option>
27 <option value="Spectral">Spectral</option>
28 <option value="Set1">Set1</option>
29 <option value="Set2">Set2</option>
30 <option value="Set3">Set3</option>
31 <option value="Dark2">Dark2</option>
32 <option value="Reds">Reds</option>
33 <option value="Oranges">Oranges</option>
34 <option value="Greens">Greens</option>
35 <option value="Blues">Blues</option>
36 <option value="Greys">Greys</option>
37 <option value="Purples">Purples</option>
38 <option value="Paired">Paired</option>
39 <option value="Pastel1">Pastel1</option>
40 <option value="Pastel2">Pastel2</option>
41 <option value="spring">spring</option>
42 <option value="summer">summer</option>
43 <option value="autumn">autumn</option>
44 <option value="winter">winter</option>
45 <option value="hot">hot</option>
46 <option value="coolwarm">coolwarm</option>
47 <option value="cool">cool</option>
48 <option value="seismic">seismic</option>
49 <option value="terrain">terrain</option>
50 <option value="ocean">ocean</option>
51 <option value="rainbow">rainbow</option>
52 <option value="bone">bone</option>
53 <option value="flag">flag</option>
54 <option value="prism">prism</option>
55 <option value="cubehelix">cubehelix</option>
56 <option value="binary">binary</option>
57 <option value="pink">pink</option>
58 <option value="gray">gray</option>
59 <option value="copper">copper</option>
60 <option value="BrBG">BrBG</option>
61 <option value="BuGn">BuGn</option>
62 <option value="BuPu">BuPu</option>
63 <option value="GnBu">GnBu</option>
64 <option value="OrRd">OrRd</option>
65 <option value="PiYG">PiYG</option>
66 <option value="PRGn">PRGn</option>
67 <option value="PuOr">PuOr</option>
68 <option value="PuRd">PuRd</option>
69 <option value="PuBu">PuBu</option>
70 <option value="RdBu">RdBu</option>
71 <option value="RdGy">RdGy</option>
72 <option value="RdPu">RdPu</option>
73 <option value="YlGn">YlGn</option>
74 <option value="PuBuGn">PuBuGn</option>
75 <option value="RdYlGn">RdYlGn</option>
76 <option value="YlGnBu">YlGnBu</option>
77 <option value="YlOrBr">YlOrBr</option>
78 <option value="YlOrRd">YlOrRd</option>
79 <option value="gist_gray">gist_gray</option>
80 <option value="gist_stern">gist_stern</option>
81 <option value="gist_earth">gist_earth</option>
82 <option value="gist_yarg">gist_yarg</option>
83 <option value="gist_ncar">gist_ncar</option>
84 <option value="gist_rainbow">gist_rainbow</option>
85 <option value="gist_heat">gist_heat</option>
86 <option value="gnuplot">gnuplot</option>
87 <option value="gnuplot2">gnuplot2</option>
88 <option value="CMRmap">CMRmap</option>
89 <option value="bwr">bwr</option>
90 <option value="hsv">hsv</option>
91 <option value="brg">brg</option>
92 <option value="jet">jet</option>
93 <option value="afmhot">afmhot</option>
94 <option value="Accent_r">Accent reversed</option>
95 <option value="Spectral_r">Spectral reversed</option>
96 <option value="Set1_r">Set1 reversed</option>
97 <option value="Set2_r">Set2 reversed</option>
98 <option value="Set3_r">Set3 reversed</option>
99 <option value="Dark2_r">Dark2 reversed</option>
100 <option value="Reds_r">Reds reversed</option>
101 <option value="Oranges_r">Oranges reversed</option>
102 <option value="Greens_r">Greens reversed</option>
103 <option value="Blues_r">Blues reversed</option>
104 <option value="Greys_r">Greys reversed</option>
105 <option value="Purples_r">Purples reversed</option>
106 <option value="Paired_r">Paired reversed</option>
107 <option value="Pastel1_r">Pastel1 reversed</option>
108 <option value="Pastel2_r">Pastel2 reversed</option>
109 <option value="spring_r">spring reversed</option>
110 <option value="summer_r">summer reversed</option>
111 <option value="autumn_r">autumn reversed</option>
112 <option value="winter_r">winter reversed</option>
113 <option value="hot_r">hot reversed</option>
114 <option value="coolwarm_r">coolwarm reversed</option>
115 <option value="cool_r">cool reversed</option>
116 <option value="seismic_r">seismic reversed</option>
117 <option value="terrain_r">terrain reversed</option>
118 <option value="ocean_r">ocean reversed</option>
119 <option value="rainbow_r">rainbow reversed</option>
120 <option value="bone_r">bone reversed</option>
121 <option value="flag_r">flag reversed</option>
122 <option value="prism_r">prism reversed</option>
123 <option value="cubehelix_r">cubehelix reversed</option>
124 <option value="binary_r">binary reversed</option>
125 <option value="pink_r">pink reversed</option>
126 <option value="gray_r">gray reversed</option>
127 <option value="copper_r">copper reversed</option>
128 <option value="BrBG_r">BrBG reversed</option>
129 <option value="BuGn_r">BuGn reversed</option>
130 <option value="BuPu_r">BuPu reversed</option>
131 <option value="GnBu_r">GnBu reversed</option>
132 <option value="OrRd_r">OrRd reversed</option>
133 <option value="PiYG_r">PiYG reversed</option>
134 <option value="PRGn_r">PRGn reversed</option>
135 <option value="PuOr_r">PuOr reversed</option>
136 <option value="PuRd_r">PuRd reversed</option>
137 <option value="PuBu_r">PuBu reversed</option>
138 <option value="RdBu_r">RdBu reversed</option>
139 <option value="RdGy_r">RdGy reversed</option>
140 <option value="RdPu_r">RdPu reversed</option>
141 <option value="YlGn_r">YlGn reversed</option>
142 <option value="PuBuGn_r">PuBuGn reversed</option>
143 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
144 <option value="RdYlGn_r">RdYlGn reversed</option>
145 <option value="YlGnBu_r">YlGnBu reversed</option>
146 <option value="YlOrBr_r">YlOrBr reversed</option>
147 <option value="YlOrRd_r">YlOrRd reversed</option>
148 <option value="gist_gray_r">gist_gray reversed</option>
149 <option value="gist_stern_r">gist_stern reversed</option>
150 <option value="gist_earth_r">gist_earth reversed</option>
151 <option value="gist_yarg_r">gist_yarg reversed</option>
152 <option value="gist_ncar_r">gist_ncar reversed</option>
153 <option value="gist_rainbow_r">gist_rainbow reversed</option>
154 <option value="gist_heat_r">gist_heat reversed</option>
155 <option value="gnuplot_r">gnuplot reversed</option>
156 <option value="gnuplot2_r">gnuplot2 reversed</option>
157 <option value="CMRmap_r">CMRmap reversed</option>
158 <option value="bwr_r">bwr reversed</option>
159 <option value="hsv_r">hsv reversed</option>
160 <option value="brg_r">brg reversed</option>
161 <option value="jet_r">jet reversed</option>
162 <option value="afmhot_r">afmhot reversed</option>
163 </param>
164 </xml>
165
166
167 <xml name="multiple_input_matrices">
168 <repeat name="input_files" title="HiC Matrix files" min="2">
169 <param name="matrix" type="data" format="h5,cool"
170 label="HiC Matrix file"
171 help=""/>
172 <param name="mlabel" type="text" size="30" optional="true" value=""
173 label="Label"
174 help="Label to use in the output. If not given the dataset name will be used instead."/>
175 </repeat>
176 </xml>
177
178 <token name="@multiple_input_matrices@">
179 #set $matrices = []
180 #set $mlabels = []
181 #for $counter, $i in enumerate($input_files):
182 ln -s $i.matrix #echo str($counter)+'_matrix'#;
183 #silent $matrices.append( '%s_matrix' % $counter )
184
185 #if str($i.mlabel.value) != "":
186 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
187 #else
188 #set $mlabels += ['"%s"' % ($i.matrix.name)]
189 #end if
190 #end for
191 #set $mlabels = ' '.join($mlabels)
192 #set $matrices = ' '.join($matrices)
193 </token>
194
195
196 <xml name="region">
197 <param name="region" type="text" label="Region of the genome to limit the operation"
198 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
199 </xml>
200
201
202
203 <xml name="kmeans_clustering">
204 <conditional name="used_multiple_regions">
205 <param name="used_multiple_regions_options" type="select"
206 label="Did you compute the matrix with more than one groups of regions?"
207 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.">
208 <option value="yes">Yes, I used multiple groups of regions</option>
209 <option value="no">No, I used only one group</option>
210 </param>
211 <when value="no">
212 <conditional name="clustering">
213 <param name="clustering_options" type="select" label="Clustering algorithm">
214 <option value="none">No clustering</option>
215 <option value="kmeans">Kmeans clustering</option>
216 </param>
217 <when value="kmeans">
218 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
219 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)."/>
220 </when>
221 <when value="none" />
222 </conditional>
223 </when>
224 <when value="yes" />
225 </conditional>
226 </xml>
227
228 <token name="@KMEANS_CLUSTERING@">
229 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
230 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
231 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
232 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
233 #end if
234 #end if
235 #end if
236 </token>
237
238 <xml name="samFlag">
239 <param name="samFlag" type="integer" optional="true" value=""
240 label="Filter reads based on the SAM flag"
241 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)"/>
242 </xml>
243 <xml name="plotNumbers">
244 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
245 label="Plot the correlation value"
246 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
247 </xml>
248 <xml name="doNotExtendPairedEnds">
249 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
250 label="Do not extend paired ends"
251 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)"/>
252 </xml>
253
254 <xml name="ignoreDuplicates">
255 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
256 label="Ignore duplicates"
257 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)" />
258 </xml>
259
260 <xml name="minMappingQuality">
261 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
262 label="Minimum mapping quality"
263 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
264 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
265 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."/>
266 </xml>
267
268 <xml name="skipZeros">
269 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
270 label ="Skip zeros"
271 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)" />
272 </xml>
273
274 <xml name="fragmentLength">
275 <param name="fragmentLength" type="integer" value="300" min="1"
276 label="Fragment length used for the sequencing"
277 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
278 </xml>
279
280 <xml name="scaleFactor">
281 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
282 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
283 </xml>
284
285 <xml name="xMax">
286 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
287 label="Max value for the x-axis in counts per bin" />
288 </xml>
289
290 <xml name="filterThreshold">
291 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
292 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
293
294 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
295 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
296 </xml>
297
298
299 <xml name="pseudocount">
300 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
301 </xml>
302 <xml name='matrix_h5_cooler_macro'>
303 <param name='matrix_h5_cooler' type="data" format="h5,cool"
304 label="Matrix to compute on."/>
305
306 </xml>
307 <xml name='matrix_h5_cooler_multiple_macro'>
308 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
309 label="Matrix to compute on." multiple="True"/>
310 </xml>
311 <token name="@REFERENCES@">
312
313 .. class:: infomark
314
315 For more information on the tools, please visit our `help site`_.
316
317 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
318
319 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
320
321 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
322 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
323 .. _help site: https://hicexplorer.readthedocs.org
324
325 </token>
326
327
328 <xml name="multiple_input_bams">
329 <repeat name="input_files" title="BAM files" min="2">
330 <param name="bamfile" type="data" format="bam"
331 label="Bam file"
332 help="The BAM file must be sorted."/>
333 <param name="label" type="text" size="30" optional="true" value=""
334 label="Label"
335 help="Label to use in the output. If not given the dataset name will be used instead."/>
336 </repeat>
337 </xml>
338
339 <xml name="multiple_input_bigwigs">
340 <repeat name="input_files" title="BigWig files" min="2">
341 <param name="bigwigfile" type="data" format="bigwig"
342 label="Bigwig file"
343 help="The Bigwig file must be sorted."/>
344 <param name="label" type="text" size="30" optional="true" value=""
345 label="Label"
346 help="Label to use in the output. If not given the dataset name will be used instead."/>
347 </repeat>
348 </xml>
349
350 <xml name="plotTitle">
351 <param name="plotTitle" type="text" value="" size="30" optional="True"
352 label="Title of the plot"
353 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
354 </xml>
355
356 <token name="@multiple_input_bams@">
357 #import tempfile
358 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
359 #set files=[]
360 #set labels=[]
361 #for $i in $input_files:
362 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
363 #set $temp_input_path = $temp_input_handle.name
364 #silent $temp_input_handle.close()
365 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
366 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
367 #silent $files.append('%s.bam' % $temp_input_path)
368
369 ##set $files += [str($i.bamfile)]
370 #if str($i.label.value) != "":
371 #set $labels += ["\"%s\"" % ($i.label.value)]
372 #else
373 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
374 #end if
375 #end for
376 </token>
377
378 <token name="@multiple_input_bigwigs@">
379 #import tempfile
380 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
381 #set files=[]
382 #set labels=[]
383 #for $i in $input_files:
384 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
385 #set $temp_input_path = $temp_input_handle.name
386 #silent $temp_input_handle.close()
387 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
388 #silent $files.append('%s.bw' % $temp_input_path)
389
390 ##set $files += [str($i.bigwigfile)]
391 #if str($i.label.value) != "":
392 #set $labels += ["\"%s\"" % ($i.label.value)]
393 #else
394 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
395 #end if
396 #end for
397 </token>
398
399 <xml name="reference_genome_source">
400 <conditional name="source">
401 <param name="ref_source" type="select" label="Reference genome">
402 <option value="cached">locally cached</option>
403 <option value="history">in your history</option>
404 </param>
405 <when value="cached">
406 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
407 <options from_data_table="deepTools_seqs">
408 <filter type="sort_by" column="1" />
409 <validator type="no_options" message="No indexes are available." />
410 </options>
411 </param>
412 </when>
413 <when value="history">
414 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
415 </when>
416 </conditional>
417 </xml>
418
419 <token name="@reference_genome_source@">
420 #if $source.ref_source=="history":
421 --genome $source.input1
422 #else:
423 --genome "${source.input1_2bit.fields.path}"
424 #end if
425 </token>
426
427 <xml name="effectiveGenomeSize">
428 <conditional name="effectiveGenomeSize">
429 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
430 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.
431 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
432 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.">
433 <option value="93260000">ce10 (93260000)</option>
434 <option value="121400000">dm3 (121400000)</option>
435 <option value="2451960000" selected="true">hg19 (2451960000)</option>
436 <option value="2150570000">mm9 (2150570000)</option>
437 <option value="specific">user specified</option>
438 </param>
439 <when value="specific">
440 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
441 </when>
442 <when value="2150570000" />
443 <when value="2451960000" />
444 <when value="121400000" />
445 <when value="93260000" />
446 </conditional>
447 </xml>
448
449 <xml name="image_file_format">
450 <param name="outFileFormat" type="select" label="Image file format">
451 <option value="png" selected="true">png</option>
452 <option value="pdf">pdf</option>
453 <option value="svg">svg</option>
454 <option value="eps">eps</option>
455 <option value="emf">emf</option>
456 </param>
457 </xml>
458
459 <xml name="missingDataAsZero">
460 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
461 label ="Treat missing data as zero"
462 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." />
463 </xml>
464
465 <xml name="input_save_matrix_values">
466 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
467 </xml>
468
469 <xml name="input_graphic_output_settings">
470 <conditional name="output" >
471 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
472 <option value="no" selected="true">no</option>
473 <option value="yes">yes</option>
474 </param>
475 <when value="no" />
476 <when value="yes">
477 <yield />
478 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
479 <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."/>
480 </when>
481 </conditional>
482 </xml>
483
484 <xml name="input_image_file_format">
485 <param name="outFileFormat" type="select" label="Image file format">
486 <option value="png" selected="true">png</option>
487 <option value="pdf">pdf</option>
488 <option value="svg">svg</option>
489 <option value="eps">eps</option>
490 <option value="emf">emf</option>
491 </param>
492 </xml>
493
494 <xml name="output_image_file_format">
495 <data format="png" name="outFileName" label="${tool.name} image">
496 <change_format>
497 <when input="output.outFileFormat" value="pdf" format="pdf" />
498 <when input="output.outFileFormat" value="svg" format="svg" />
499 <when input="output.outFileFormat" value="eps" format="eps" />
500 <when input="output.outFileFormat" value="emf" format="emf" />
501 </change_format>
502 </data>
503 </xml>
504
505 <xml name="output_save_matrix_values">
506 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
507 <filter>
508 ((
509 output['showOutputSettings'] == 'yes' and
510 output['saveMatrix'] is True
511 ))
512 </filter>
513 </data>
514 </xml>
515
516 <xml name="output_graphic_outputs">
517 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
518 <filter>
519 ((
520 output['showOutputSettings'] == 'yes' and
521 output['saveData'] is True
522 ))
523 </filter>
524 </data>
525 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
526 <filter>
527 ((
528 output['showOutputSettings'] == 'yes' and
529 output['saveSortedRegions'] is True
530 ))
531 </filter>
532 </data>
533 </xml>
534
535 <xml name="track_input_h5_macro">
536 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
537 </xml>
538 <xml name="track_input_bed_macro">
539 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
540 </xml>
541 <xml name="track_input_bedgraph_macro">
542 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
543 </xml>
544 <xml name="track_input_bigwig_macro">
545 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
546 </xml>
547 <xml name="track_input_bedgraph_matrix_macro">
548 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
549 </xml>
550 <xml name="track_input_tabular_macro">
551 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
552 </xml>
553 <xml name="plot_title">
554 <param name="title" type="text" optional="true" label="Plot title"/>
555 </xml>
556
557 <xml name="spacer_macro">
558 <param name="spacer_width" type="float" value="" optional="True"
559 label="Include spacer at the end of the track." help="Width of the spacer." />
560 </xml>
561 <xml name="fontsize_macro">
562 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
563 </xml>
564 </macros>