Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

comparison macros.xml.orig @ 0:a0ab04565c73 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:37:57 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:a0ab04565c73
1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <<<<<<< HEAD
4 <token name="@WRAPPER_VERSION@">2.0</token>
5
6 <token name="@USE_RANGE@">
7 #if $use_range.select_use_range == "yes_use_range":
8 --range $range_min:$range_max
9 #end if
10 </token>
11
12 =======
13 <token name="@WRAPPER_VERSION@">2.1alpha1</token>
14 >>>>>>> joachimwolff-master
15 <xml name="requirements">
16 <requirements>
17 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
18 <yield />
19 </requirements>
20 <version_command>@BINARY@ --version</version_command>
21 </xml>
22
23 <xml name="citations">
24 <citations>
25 <citation type="doi">10.5281/zenodo.1133705</citation>
26 <yield />
27 </citations>
28 </xml>
29
30 <xml name="zMax">
31 <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 -->
32 </xml>
33 <xml name="use_range">
34 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
35 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
36 <option value="no_use_range">No restriction</option>
37 <option value="yes_use_range">Only consider counts within a range</option>
38 </param>
39 <when value="no_use_range"/>
40 <when value="yes_use_range">
41 <param name="range_min" type="integer" value="" min="0"/>
42 <param name="range_max" type="integer" value="" min="0"/>
43 </when>
44 </conditional>
45 </xml>
46 <xml name="colormap">
47 <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">
48 <option value="RdYlBu">RdYlBu</option>
49 <option value="Accent">Accent</option>
50 <option value="Spectral">Spectral</option>
51 <option value="Set1">Set1</option>
52 <option value="Set2">Set2</option>
53 <option value="Set3">Set3</option>
54 <option value="Dark2">Dark2</option>
55 <option value="Reds">Reds</option>
56 <option value="Oranges">Oranges</option>
57 <option value="Greens">Greens</option>
58 <option value="Blues">Blues</option>
59 <option value="Greys">Greys</option>
60 <option value="Purples">Purples</option>
61 <option value="Paired">Paired</option>
62 <option value="Pastel1">Pastel1</option>
63 <option value="Pastel2">Pastel2</option>
64 <option value="spring">spring</option>
65 <option value="summer">summer</option>
66 <option value="autumn">autumn</option>
67 <option value="winter">winter</option>
68 <option value="hot">hot</option>
69 <option value="coolwarm">coolwarm</option>
70 <option value="cool">cool</option>
71 <option value="seismic">seismic</option>
72 <option value="terrain">terrain</option>
73 <option value="ocean">ocean</option>
74 <option value="rainbow">rainbow</option>
75 <option value="bone">bone</option>
76 <option value="flag">flag</option>
77 <option value="prism">prism</option>
78 <option value="cubehelix">cubehelix</option>
79 <option value="binary">binary</option>
80 <option value="pink">pink</option>
81 <option value="gray">gray</option>
82 <option value="copper">copper</option>
83 <option value="BrBG">BrBG</option>
84 <option value="BuGn">BuGn</option>
85 <option value="BuPu">BuPu</option>
86 <option value="GnBu">GnBu</option>
87 <option value="OrRd">OrRd</option>
88 <option value="PiYG">PiYG</option>
89 <option value="PRGn">PRGn</option>
90 <option value="PuOr">PuOr</option>
91 <option value="PuRd">PuRd</option>
92 <option value="PuBu">PuBu</option>
93 <option value="RdBu">RdBu</option>
94 <option value="RdGy">RdGy</option>
95 <option value="RdPu">RdPu</option>
96 <option value="YlGn">YlGn</option>
97 <option value="PuBuGn">PuBuGn</option>
98 <option value="RdYlGn">RdYlGn</option>
99 <option value="YlGnBu">YlGnBu</option>
100 <option value="YlOrBr">YlOrBr</option>
101 <option value="YlOrRd">YlOrRd</option>
102 <option value="gist_gray">gist_gray</option>
103 <option value="gist_stern">gist_stern</option>
104 <option value="gist_earth">gist_earth</option>
105 <option value="gist_yarg">gist_yarg</option>
106 <option value="gist_ncar">gist_ncar</option>
107 <option value="gist_rainbow">gist_rainbow</option>
108 <option value="gist_heat">gist_heat</option>
109 <option value="gnuplot">gnuplot</option>
110 <option value="gnuplot2">gnuplot2</option>
111 <option value="CMRmap">CMRmap</option>
112 <option value="bwr">bwr</option>
113 <option value="hsv">hsv</option>
114 <option value="brg">brg</option>
115 <option value="jet">jet</option>
116 <option value="afmhot">afmhot</option>
117 <option value="Accent_r">Accent reversed</option>
118 <option value="Spectral_r">Spectral reversed</option>
119 <option value="Set1_r">Set1 reversed</option>
120 <option value="Set2_r">Set2 reversed</option>
121 <option value="Set3_r">Set3 reversed</option>
122 <option value="Dark2_r">Dark2 reversed</option>
123 <option value="Reds_r">Reds reversed</option>
124 <option value="Oranges_r">Oranges reversed</option>
125 <option value="Greens_r">Greens reversed</option>
126 <option value="Blues_r">Blues reversed</option>
127 <option value="Greys_r">Greys reversed</option>
128 <option value="Purples_r">Purples reversed</option>
129 <option value="Paired_r">Paired reversed</option>
130 <option value="Pastel1_r">Pastel1 reversed</option>
131 <option value="Pastel2_r">Pastel2 reversed</option>
132 <option value="spring_r">spring reversed</option>
133 <option value="summer_r">summer reversed</option>
134 <option value="autumn_r">autumn reversed</option>
135 <option value="winter_r">winter reversed</option>
136 <option value="hot_r">hot reversed</option>
137 <option value="coolwarm_r">coolwarm reversed</option>
138 <option value="cool_r">cool reversed</option>
139 <option value="seismic_r">seismic reversed</option>
140 <option value="terrain_r">terrain reversed</option>
141 <option value="ocean_r">ocean reversed</option>
142 <option value="rainbow_r">rainbow reversed</option>
143 <option value="bone_r">bone reversed</option>
144 <option value="flag_r">flag reversed</option>
145 <option value="prism_r">prism reversed</option>
146 <option value="cubehelix_r">cubehelix reversed</option>
147 <option value="binary_r">binary reversed</option>
148 <option value="pink_r">pink reversed</option>
149 <option value="gray_r">gray reversed</option>
150 <option value="copper_r">copper reversed</option>
151 <option value="BrBG_r">BrBG reversed</option>
152 <option value="BuGn_r">BuGn reversed</option>
153 <option value="BuPu_r">BuPu reversed</option>
154 <option value="GnBu_r">GnBu reversed</option>
155 <option value="OrRd_r">OrRd reversed</option>
156 <option value="PiYG_r">PiYG reversed</option>
157 <option value="PRGn_r">PRGn reversed</option>
158 <option value="PuOr_r">PuOr reversed</option>
159 <option value="PuRd_r">PuRd reversed</option>
160 <option value="PuBu_r">PuBu reversed</option>
161 <option value="RdBu_r">RdBu reversed</option>
162 <option value="RdGy_r">RdGy reversed</option>
163 <option value="RdPu_r">RdPu reversed</option>
164 <option value="YlGn_r">YlGn reversed</option>
165 <option value="PuBuGn_r">PuBuGn reversed</option>
166 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
167 <option value="RdYlGn_r">RdYlGn reversed</option>
168 <option value="YlGnBu_r">YlGnBu reversed</option>
169 <option value="YlOrBr_r">YlOrBr reversed</option>
170 <option value="YlOrRd_r">YlOrRd reversed</option>
171 <option value="gist_gray_r">gist_gray reversed</option>
172 <option value="gist_stern_r">gist_stern reversed</option>
173 <option value="gist_earth_r">gist_earth reversed</option>
174 <option value="gist_yarg_r">gist_yarg reversed</option>
175 <option value="gist_ncar_r">gist_ncar reversed</option>
176 <option value="gist_rainbow_r">gist_rainbow reversed</option>
177 <option value="gist_heat_r">gist_heat reversed</option>
178 <option value="gnuplot_r">gnuplot reversed</option>
179 <option value="gnuplot2_r">gnuplot2 reversed</option>
180 <option value="CMRmap_r">CMRmap reversed</option>
181 <option value="bwr_r">bwr reversed</option>
182 <option value="hsv_r">hsv reversed</option>
183 <option value="brg_r">brg reversed</option>
184 <option value="jet_r">jet reversed</option>
185 <option value="afmhot_r">afmhot reversed</option>
186 </param>
187 </xml>
188
189
190 <xml name="multiple_input_matrices">
191 <repeat name="input_files" title="HiC Matrix files" min="2">
192 <param name="matrix" type="data" format="h5,cool"
193 label="HiC Matrix file"
194 help=""/>
195 <param name="mlabel" type="text" size="30" optional="true" value=""
196 label="Label"
197 help="Label to use in the output. If not given the dataset name will be used instead."/>
198 </repeat>
199 </xml>
200
201 <token name="@multiple_input_matrices@">
202 #set $matrices = []
203 #set $mlabels = []
204 #for $counter, $i in enumerate($input_files):
205 ln -s $i.matrix #echo str($counter)+'_matrix'#;
206 #silent $matrices.append( '%s_matrix' % $counter )
207
208 #if str($i.mlabel.value) != "":
209 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
210 #else
211 #set $mlabels += ['"%s"' % ($i.matrix.name)]
212 #end if
213 #end for
214 #set $mlabels = ' '.join($mlabels)
215 #set $matrices = ' '.join($matrices)
216 </token>
217
218
219 <xml name="region">
220 <param name="region" type="text" label="Region of the genome to limit the operation"
221 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
222 </xml>
223
224
225
226 <xml name="kmeans_clustering">
227 <conditional name="used_multiple_regions">
228 <param name="used_multiple_regions_options" type="select"
229 label="Did you compute the matrix with more than one groups of regions?"
230 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.">
231 <option value="yes">Yes, I used multiple groups of regions</option>
232 <option value="no">No, I used only one group</option>
233 </param>
234 <when value="no">
235 <conditional name="clustering">
236 <param name="clustering_options" type="select" label="Clustering algorithm">
237 <option value="none">No clustering</option>
238 <option value="kmeans">Kmeans clustering</option>
239 </param>
240 <when value="kmeans">
241 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
242 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)."/>
243 </when>
244 <when value="none" />
245 </conditional>
246 </when>
247 <when value="yes" />
248 </conditional>
249 </xml>
250
251 <token name="@KMEANS_CLUSTERING@">
252 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
253 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
254 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
255 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
256 #end if
257 #end if
258 #end if
259 </token>
260
261 <xml name="samFlag">
262 <param name="samFlag" type="integer" optional="true" value=""
263 label="Filter reads based on the SAM flag"
264 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)"/>
265 </xml>
266 <xml name="plotNumbers">
267 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
268 label="Plot the correlation value"
269 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
270 </xml>
271 <xml name="doNotExtendPairedEnds">
272 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
273 label="Do not extend paired ends"
274 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)"/>
275 </xml>
276
277 <xml name="ignoreDuplicates">
278 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
279 label="Ignore duplicates"
280 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)" />
281 </xml>
282
283 <xml name="minMappingQuality">
284 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
285 label="Minimum mapping quality"
286 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
287 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
288 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."/>
289 </xml>
290
291 <xml name="skipZeros">
292 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
293 label ="Skip zeros"
294 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)" />
295 </xml>
296
297 <xml name="fragmentLength">
298 <param name="fragmentLength" type="integer" value="300" min="1"
299 label="Fragment length used for the sequencing"
300 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
301 </xml>
302
303 <xml name="scaleFactor">
304 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
305 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
306 </xml>
307
308 <xml name="xMax">
309 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
310 label="Max value for the x-axis in counts per bin" />
311 </xml>
312
313 <xml name="filterThreshold">
314 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
315 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
316
317 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
318 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
319 </xml>
320
321 <xml name="pseudocount">
322 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
323 </xml>
324 <xml name='matrix_h5_cooler_macro'>
325 <param name='matrix_h5_cooler' type="data" format="h5,cool"
326 label="Matrix to compute on"/>
327 </xml>
328 <xml name='matrix_h5_cooler_multiple_macro'>
329 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
330 label="Matricies to compute on" multiple="true"/>
331 </xml>
332 <token name="@REFERENCES@">
333
334 .. class:: infomark
335
336 For more information on the tools, please visit our `help site`_.
337
338 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
339
340 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
341
342 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
343 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
344 .. _help site: https://hicexplorer.readthedocs.org
345
346 </token>
347
348
349 <xml name="multiple_input_bams">
350 <repeat name="input_files" title="BAM files" min="2">
351 <param name="bamfile" type="data" format="bam"
352 label="Bam file"
353 help="The BAM file must be sorted."/>
354 <param name="label" type="text" size="30" optional="true" value=""
355 label="Label"
356 help="Label to use in the output. If not given the dataset name will be used instead."/>
357 </repeat>
358 </xml>
359
360 <xml name="multiple_input_bigwigs">
361 <repeat name="input_files" title="BigWig files" min="2">
362 <param name="bigwigfile" type="data" format="bigwig"
363 label="Bigwig file"
364 help="The Bigwig file must be sorted."/>
365 <param name="label" type="text" size="30" optional="true" value=""
366 label="Label"
367 help="Label to use in the output. If not given the dataset name will be used instead."/>
368 </repeat>
369 </xml>
370
371 <xml name="plotTitle">
372 <param name="plotTitle" type="text" value="" size="30" optional="True"
373 label="Title of the plot"
374 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
375 </xml>
376
377 <token name="@multiple_input_bams@">
378 #import tempfile
379 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
380 #set files=[]
381 #set labels=[]
382 #for $i in $input_files:
383 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
384 #set $temp_input_path = $temp_input_handle.name
385 #silent $temp_input_handle.close()
386 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
387 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
388 #silent $files.append('%s.bam' % $temp_input_path)
389
390 ##set $files += [str($i.bamfile)]
391 #if str($i.label.value) != "":
392 #set $labels += ["\"%s\"" % ($i.label.value)]
393 #else
394 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
395 #end if
396 #end for
397 </token>
398
399 <token name="@multiple_input_bigwigs@">
400 #import tempfile
401 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
402 #set files=[]
403 #set labels=[]
404 #for $i in $input_files:
405 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
406 #set $temp_input_path = $temp_input_handle.name
407 #silent $temp_input_handle.close()
408 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
409 #silent $files.append('%s.bw' % $temp_input_path)
410
411 ##set $files += [str($i.bigwigfile)]
412 #if str($i.label.value) != "":
413 #set $labels += ["\"%s\"" % ($i.label.value)]
414 #else
415 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
416 #end if
417 #end for
418 </token>
419
420 <xml name="reference_genome_source">
421 <conditional name="source">
422 <param name="ref_source" type="select" label="Reference genome">
423 <option value="cached">locally cached</option>
424 <option value="history">in your history</option>
425 </param>
426 <when value="cached">
427 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
428 <options from_data_table="deepTools_seqs">
429 <filter type="sort_by" column="1" />
430 <validator type="no_options" message="No indexes are available." />
431 </options>
432 </param>
433 </when>
434 <when value="history">
435 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
436 </when>
437 </conditional>
438 </xml>
439
440 <token name="@reference_genome_source@">
441 #if $source.ref_source=="history":
442 --genome $source.input1
443 #else:
444 --genome "${source.input1_2bit.fields.path}"
445 #end if
446 </token>
447
448 <xml name="effectiveGenomeSize">
449 <conditional name="effectiveGenomeSize">
450 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
451 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.
452 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
453 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.">
454 <option value="93260000">ce10 (93260000)</option>
455 <option value="121400000">dm3 (121400000)</option>
456 <option value="2451960000" selected="true">hg19 (2451960000)</option>
457 <option value="2150570000">mm9 (2150570000)</option>
458 <option value="specific">user specified</option>
459 </param>
460 <when value="specific">
461 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
462 </when>
463 <when value="2150570000" />
464 <when value="2451960000" />
465 <when value="121400000" />
466 <when value="93260000" />
467 </conditional>
468 </xml>
469
470 <xml name="image_file_format">
471 <param name="outFileFormat" type="select" label="Image file format">
472 <option value="png" selected="true">png</option>
473 <option value="pdf">pdf</option>
474 <option value="svg">svg</option>
475 <option value="eps">eps</option>
476 <option value="emf">emf</option>
477 </param>
478 </xml>
479
480 <xml name="missingDataAsZero">
481 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
482 label ="Treat missing data as zero"
483 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." />
484 </xml>
485
486 <xml name="input_save_matrix_values">
487 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
488 </xml>
489
490 <xml name="input_graphic_output_settings">
491 <conditional name="output" >
492 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
493 <option value="no" selected="true">no</option>
494 <option value="yes">yes</option>
495 </param>
496 <when value="no" />
497 <when value="yes">
498 <yield />
499 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
500 <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."/>
501 </when>
502 </conditional>
503 </xml>
504
505 <xml name="input_image_file_format">
506 <param name="outFileFormat" type="select" label="Image file format">
507 <option value="png" selected="true">png</option>
508 <option value="pdf">pdf</option>
509 <option value="svg">svg</option>
510 <option value="eps">eps</option>
511 <option value="emf">emf</option>
512 </param>
513 </xml>
514
515 <xml name="output_image_file_format">
516 <data format="png" name="outFileName" label="${tool.name} image">
517 <change_format>
518 <when input="output.outFileFormat" value="pdf" format="pdf" />
519 <when input="output.outFileFormat" value="svg" format="svg" />
520 <when input="output.outFileFormat" value="eps" format="eps" />
521 <when input="output.outFileFormat" value="emf" format="emf" />
522 </change_format>
523 </data>
524 </xml>
525
526 <xml name="output_save_matrix_values">
527 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
528 <filter>
529 ((
530 output['showOutputSettings'] == 'yes' and
531 output['saveMatrix'] is True
532 ))
533 </filter>
534 </data>
535 </xml>
536
537 <xml name="output_graphic_outputs">
538 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
539 <filter>
540 ((
541 output['showOutputSettings'] == 'yes' and
542 output['saveData'] is True
543 ))
544 </filter>
545 </data>
546 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
547 <filter>
548 ((
549 output['showOutputSettings'] == 'yes' and
550 output['saveSortedRegions'] is True
551 ))
552 </filter>
553 </data>
554 </xml>
555
556 <xml name="track_input_h5_macro">
557 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
558 </xml>
559 <xml name="track_input_bed_macro">
560 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
561 </xml>
562 <xml name="track_input_bedgraph_macro">
563 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
564 </xml>
565 <xml name="track_input_bigwig_macro">
566 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
567 </xml>
568 <xml name="track_input_bedgraph_matrix_macro">
569 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
570 </xml>
571 <xml name="track_input_tabular_macro">
572 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
573 </xml>
574 <xml name="plot_title">
575 <param name="title" type="text" optional="true" label="Plot title"/>
576 </xml>
577
578 <xml name="spacer_macro">
579 <param name="spacer_width" type="float" value="" optional="True"
580 label="Include spacer at the end of the track." help="Width of the spacer." />
581 </xml>
582 <xml name="fontsize_macro">
583 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
584 </xml>
585 </macros>