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comparison deepTools_macros.xml @ 0:9987ddd67710 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5
author bgruening
date Fri, 19 May 2023 08:30:42 +0000
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children f6f246438eda
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-1:000000000000 0:9987ddd67710
1 <macros>
2
3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
4 <token name="@WRAPPER_VERSION@">3.5.1.0</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="3.5.1">deeptools</requirement>
8 <requirement type="package" version="1.9">samtools</requirement>
9 </requirements>
10 <expand macro="stdio" />
11 <version_command>@BINARY@ --version</version_command>
12 </xml>
13
14 <xml name="advancedOpt_scaffold">
15 <conditional name="advancedOpt">
16 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
17 <option value="no" selected="true">no</option>
18 <option value="yes">yes</option>
19 </param>
20 <when value="no" />
21 <when value="yes">
22 <yield/>
23 </when>
24 </conditional>
25 </xml>
26
27 <token name="@PLOTWIDTHHEIGHT@">
28 --plotWidth '$advancedOpt.plotWidth'
29 --plotHeight '$advancedOpt.plotHeight'
30 </token>
31
32 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
33 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
34 label="Plot height"
35 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
36
37 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
38 label="Plot width"
39 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
40 </xml>
41
42 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
43 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
44 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
45 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
46 --extendReads
47 #end if
48 $advancedOpt.ignoreDuplicates
49 $advancedOpt.centerReads
50 #if $advancedOpt.minMappingQuality:
51 --minMappingQuality '$advancedOpt.minMappingQuality'
52 #end if
53 #if $advancedOpt.samFlagInclude:
54 --samFlagInclude $advancedOpt.samFlagInclude
55 #end if
56 #if $advancedOpt.samFlagExclude:
57 --samFlagExclude $advancedOpt.samFlagExclude
58 #end if
59 #if $advancedOpt.minFragmentLength:
60 --minFragmentLength $advancedOpt.minFragmentLength
61 #end if
62 #if $advancedOpt.maxFragmentLength:
63 --maxFragmentLength $advancedOpt.maxFragmentLength
64 #end if
65 </token>
66
67 <token name="@ADVANCED_OPTS_GTF@">
68 $advancedOpt.metagene
69 #if $advancedOpt.transcriptID:
70 --transcriptID $advancedOpt.transcriptID
71 #end if
72 #if $advancedOpt.exonID:
73 --exonID $advancedOpt.exonID
74 #end if
75 #if $advancedOpt.transcript_id_designator:
76 --transcript_id_designator $advancedOpt.transcript_id_designator
77 #end if
78 </token>
79
80 <xml name="heatmap_options">
81 <expand macro="zMin_zMax" />
82 <expand macro="colorMap" />
83 <expand macro="plotTitle" />
84 <expand macro="plotNumbers" />
85 </xml>
86
87 <token name="@HEATMAP_OPTIONS@">
88 #if str($plotting_type.zMin) != "":
89 --zMin $plotting_type.zMin
90 #end if
91 #if str($plotting_type.zMax) != "":
92 --zMax $plotting_type.zMax
93 #end if
94 --colorMap '$plotting_type.colorMap'
95 $plotting_type.plotNumbers
96 --plotTitle '$plotting_type.plotTitle'
97 </token>
98
99
100 <xml name="includeZeros">
101 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
102 label="Include zeros"
103 help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." />
104 </xml>
105
106 <xml name="zMin_zMax">
107 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
108 help="If not specified the value is set automatically."/>
109 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
110 help="If not specified the value is set automatically."/>
111 </xml>
112
113 <xml name="region_limit_operation">
114 <param argument="--region" type="text" value=""
115 label="Region of the genome to limit the operation to"
116 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
117 <sanitizer>
118 <valid initial="string.letters,string.digits">
119 <add value="|"/>
120 <add value=":"/>
121 <add value="."/>
122 </valid>
123 </sanitizer>
124 </param>
125 </xml>
126
127 <xml name="smoothLength">
128 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
129 label="Smooth values using the following length (in bases)"
130 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
131 </xml>
132
133
134 <xml name="kmeans_clustering">
135 <conditional name="used_multiple_regions">
136 <param name="used_multiple_regions_options" type="select"
137 label="Did you compute the matrix with more than one groups of regions?"
138 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.">
139 <option value="yes">Yes, I used multiple groups of regions</option>
140 <option value="no">No, I used only one group</option>
141 </param>
142 <when value="no">
143 <conditional name="clustering">
144 <param name="clustering_options" type="select" label="Clustering algorithm">
145 <option value="none">No clustering</option>
146 <option value="kmeans">Kmeans clustering</option>
147 <option value="hclust">Hierarchical clustering</option>
148 </param>
149 <when value="kmeans">
150 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
151 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
152 This only works for data that is not grouped, otherwise only the first group will be clustered.
153 If more specific clustering methods are required it is advisable to save the underlying matrix and
154 run the clustering using other software."/>
155 </when>
156 <when value="hclust">
157 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
158 help="WARNING: This option causes the tool to run for a very long time! When this option is
159 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
160 This only works for data that is not grouped, otherwise only the first group will be clustered.
161 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
162 If more specific clustering methods are required it is advisable to save the underlying matrix and
163 run the clustering using other software."/>
164 </when>
165 <when value="none" />
166 </conditional>
167 <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
168 label="Compute the silhouette score for each region"
169 help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
170 The silhouette score is a measure of how similar a region is to other regions in the same cluster as
171 opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
172 The silhouette evaluation can be very slow when you have more than 100 000 regions." />
173 </when>
174 <when value="yes" />
175 </conditional>
176 </xml>
177
178 <token name="@KMEANS_CLUSTERING@">
179 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
180 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
181 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
182 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
183 #end if
184 #end if
185 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
186 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
187 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
188 #end if
189 #end if
190 $advancedOpt.used_multiple_regions.silhouette
191 #end if
192 </token>
193
194 <xml name="samFlags">
195 <param argument="--samFlagInclude" type="integer" optional="True" value=""
196 label="Include reads based on the SAM flag"
197 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."/>
198 <param argument="--samFlagExclude" type="integer" optional="True" value=""
199 label="Exclude reads based on the SAM flag"
200 help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
201 </xml>
202
203 <xml name="fragLength">
204 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
205 label="Minimum fragment length for inclusion."
206 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
207 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
208 label="Maximum fragment length for inclusion."
209 help="A value of 0 (the default) is equivalent to no maximum." />
210 </xml>
211
212 <xml name="read_processing_options">
213 <expand macro="extendReads" />
214 <expand macro="ignoreDuplicates" />
215 <expand macro="centerReads" />
216 <expand macro="minMappingQuality" />
217 <expand macro="samFlags" />
218 <expand macro="fragLength" />
219 </xml>
220
221 <xml name="gtf_options">
222 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
223 label="Use a metagene model"
224 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
225 <param argument="--transcriptID" optional="True" value="transcript" type="text"
226 label="transcript designator"
227 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" />
228 <param argument="--exonID" optional="True" value="exon" type="text"
229 label="exon designator"
230 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" />
231 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
232 label="transcriptID key designator"
233 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
234 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
235 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
236 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
237 </xml>
238
239
240 <xml name="plotNumbers">
241 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
242 label="Plot the correlation value"
243 help="If set, then the correlation number is plotted on top of the heatmap."/>
244 </xml>
245
246 <xml name="extendReads">
247 <conditional name="doExtendCustom">
248 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
249 help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.
250 By default *each* read mate is extended.
251 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
252 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
253 Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not
254 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
255 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
256 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
257 <option value="custom">A custom length, which will be applied to ALL reads.</option>
258 </param>
259 <when value="no" />
260 <when value="yes" />
261 <when value="custom">
262 <param name="extendReadsValue" type="integer" value="300" min="1"
263 label="Extend reads to the given average fragment size"
264 help="Extend all reads to this length" />
265 </when>
266 </conditional>
267 </xml>
268
269 <xml name="corMethod">
270 <param argument="--corMethod" type="select" label="Correlation method">
271 <option value="spearman" selected="True">Spearman</option>
272 <option value="pearson">Pearson</option>
273 </param>
274 </xml>
275
276 <xml name="distanceBetweenBins">
277 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
278 label="Distance between bins"
279 help="By default, multiBamSummary considers consecutive bins of
280 the specified 'Bin size'. However, to reduce the
281 computation time, a larger distance between bins can
282 be given. Larger distances result in fewer bins being
283 considered."/>
284 </xml>
285
286 <xml name="centerReads">
287 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
288 label="Center regions with respect to the fragment length"
289 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/>
290 </xml>
291
292 <xml name="ignoreDuplicates">
293 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
294 label="Ignore duplicates"
295 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." />
296 </xml>
297
298 <xml name="sortUsing">
299 <param argument="--sortUsing" type="select" label="Method used for sorting"
300 help="For each row the method is computed.">
301 <option value="mean" selected="true">mean</option>
302 <option value="median">median</option>
303 <option value="min">min</option>
304 <option value="max">max</option>
305 <option value="sum">sum</option>
306 <option value="region_length">region length</option>
307 </param>
308 </xml>
309
310 <xml name="sortRegionsComputeMatrix">
311 <param argument="--sortRegions" type="select" label="Sort regions"
312 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
313 <option value="no">no ordering</option>
314 <option value="keep" selected="true">maintain the same ordering as the input files</option>
315 <option value="descend">descending order</option>
316 <option value="ascend">ascending order</option>
317 </param>
318 </xml>
319
320 <xml name="sortRegions">
321 <param argument="--sortRegions" type="select" label="Sort regions"
322 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
323 <option value="no">maintain the same ordering as the input files</option>
324 <option value="descend" selected="true">descending order</option>
325 <option value="ascend">ascending order</option>
326 </param>
327 </xml>
328
329 <xml name="minMappingQuality">
330 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
331 label="Minimum mapping quality"
332 help= "If set, only reads with a mapping quality score at least this high are considered."/>
333 </xml>
334
335 <xml name="skipZeros">
336 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
337 label ="Skip zeros"
338 help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." />
339 </xml>
340
341 <xml name="fragmentLength">
342 <param argument="--fragmentLength" type="integer" min="1" optional="true"
343 label="Fragment length used for the sequencing"
344 help ="If paired-end reads are used, the fragment length is computed from the BAM/CRAM file, so this is only needed for single-end data."/>
345 </xml>
346
347 <xml name="scaleFactor">
348 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
349 help="The computed scaling factor will be multiplied by this (default 1)." />
350 </xml>
351
352 <xml name="scaleFactors">
353 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
354 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
355 </xml>
356
357 <xml name="stdio">
358 <stdio>
359 <exit_code range="1:" />
360 <exit_code range=":-1" />
361 <regex match="Error:" />
362 <regex match="Exception:" />
363 <regex match="EXception:" />
364 <regex match="Traceback" />
365 </stdio>
366 </xml>
367
368 <xml name="pseudocount">
369 <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
370 </xml>
371 <token name="@REFERENCES@">
372
373 .. class:: infomark
374
375 For more information on the tools, please visit our `help site`_.
376
377 For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
378
379 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
380
381 .. _Biostars: http://biostars.org
382 .. _on github: http://github.com
383 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
384 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
385 .. _help site: https://deeptools.readthedocs.org/
386
387 </token>
388 <xml name="citations">
389 <citations>
390 <citation type="doi">10.1093/nar/gkw257</citation>
391 <yield />
392 </citations>
393 </xml>
394
395 <xml name="multiple_input_bams" tokens="MIN">
396 <conditional name="multibam_conditional">
397 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
398 <option value="No" selected="true">No</option>
399 <option value="Yes">Yes</option>
400 </param>
401 <when value="No">
402 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
403 label="BAM/CRAM file" multiple="true"
404 help=""/>
405 </when>
406 <when value="Yes">
407 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
408 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
409 </repeat>
410 </when>
411 </conditional>
412 </xml>
413
414 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
415 <conditional name="multibigwig_conditional">
416 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
417 is vital to you, select Yes below.">
418 <option value="No" selected="true">No</option>
419 <option value="Yes">Yes</option>
420 </param>
421 <when value="No">
422 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
423 label="@LABEL@"
424 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
425 </when>
426 <when value="Yes">
427 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
428 <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
429 </repeat>
430 </when>
431 </conditional>
432 </xml>
433
434 <xml name="custom_sample_labels">
435 <conditional name="custom_sample_labels_conditional">
436 <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used.">
437 <option value="No" selected="true">No, use sample names in the history</option>
438 <option value="Yes">Yes, I want to specify new labels</option>
439 </param>
440 <when value="No">
441 </when>
442 <when value="Yes">
443 <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., &quot;sample 1&quot; &quot;sample 2&quot;)">
444 <sanitizer>
445 <valid initial="string.printable">
446 </valid>
447 </sanitizer>
448 </param>
449 </when>
450 </conditional>
451 </xml>
452
453 <xml name="plotTitle">
454 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
455 label="Title of the plot"
456 help="Title of the plot, to be printed on top of the generated image." />
457 </xml>
458
459 <xml name="legendLocation">
460 <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile.">
461 <option value="best" selected="true">Best (automatic)</option>
462 <option value="upper-right">upper-right</option>
463 <option value="upper-left">upper-left</option>
464 <option value="upper-center">upper-center</option>
465 <option value="lower-right">lower-right</option>
466 <option value="lower-left">lower-left</option>
467 <option value="lower-center">lower-center</option>
468 <option value="center-right">center-right</option>
469 <option value="center-left">center-left</option>
470 <option value="center">center</option>
471 <option value="none">none (only works for heatmaps</option>
472 </param>
473 </xml>
474
475 <xml name="labelRotation">
476 <param argument="--labelRotation" type="integer" value="0"
477 label="Rotation of the X-axis labels (in degrees)"
478 help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." />
479 </xml>
480
481
482 <token name="@multiple_input_bams@">
483 <![CDATA[
484 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
485 #set custom_labels=$custom_sample_labels_conditional.labels
486 #end if
487 #set files=[]
488 #set labels=[]
489 #import re
490 #if $multibam_conditional.orderMatters == "No":
491 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
492 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
493 ln -s '${bamfile}' './${counter}.bam' &&
494 #if $bamfile.ext == 'bam':
495 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
496 #else:
497 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
498 #end if
499 #silent $files.append("'%s.bam'" % $counter)
500 #silent $labels.append("'%s'" % $identifier)
501 #end for
502 #else:
503 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
504 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
505 ln -s '${f.bamfiles}' './${counter}.bam' &&
506 #if $f.bamfiles.ext == 'bam':
507 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
508 #else:
509 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
510 #end if
511 #silent $files.append("'%s.bam'" % $counter)
512 #silent $labels.append("'%s'" % $identifier)
513 #end for
514 #end if
515 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
516 #set labels=custom_labels
517 #end if
518 ]]>
519 </token>
520
521 <token name="@multiple_input_bigwigs@">
522 <![CDATA[
523 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
524 #set custom_labels=$custom_sample_labels_conditional.labels
525 #end if
526 #set files=[]
527 #set labels=[]
528 #import re
529 #if $multibigwig_conditional.orderMatters == "No":
530 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
531 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
532 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
533 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
534 #silent $labels.append("'%s'" % $identifier)
535 #end for
536 #else:
537 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
538 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
539 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
540 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
541 #silent $labels.append("'%s'" % $identifier)
542 #end for
543 #end if
544 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
545 #set labels=custom_labels
546 #end if
547 ]]>
548 </token>
549
550 <xml name="blacklist">
551 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
552 label="Blacklisted regions in BED/GTF format"
553 help="One or more files containing regions to exclude from the analysis" />
554 </xml>
555
556 <token name="@blacklist@">
557 <![CDATA[
558 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
559 #set blfiles=[]
560 #for $f in $advancedOpt.blackListFileName:
561 #silent $blfiles.append("'%s'" % $f)
562 #end for
563 #if $blfiles != ["'None'"]:
564 --blackListFileName #echo ' '.join($blfiles)#
565 #end if
566 #end if
567 ]]>
568 </token>
569
570 <xml name="multiple_bed">
571 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
572 label="Regions in BED/GTF format"
573 help="One or more files containing regions to include in the analysis" />
574 </xml>
575
576 <token name="@multiple_bed@">
577 <![CDATA[
578 #set files=[]
579 #set labels=[]
580 #for $f in $BED:
581 #silent $files.append("'%s'" % $f)
582 #silent $labels.append("'%s'" % $f.display_name)
583 #end for
584 #if len($files) > 0:
585 --BED #echo ' '.join($files)#
586 --regionLabels #echo ' '.join($labels)#
587 #end if
588 ]]>
589 </token>
590
591 <xml name="reference_genome_source">
592 <conditional name="source">
593 <param name="ref_source" type="select" label="Reference genome">
594 <option value="cached">locally cached</option>
595 <option value="history">in your history</option>
596 </param>
597 <when value="cached">
598 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
599 <options from_data_table="lastz_seqs">
600 <filter type="sort_by" column="1" />
601 <validator type="no_options" message="No indexes are available." />
602 </options>
603 </param>
604 </when>
605 <when value="history">
606 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
607 </when>
608 </conditional>
609 </xml>
610
611 <token name="@reference_genome_source@">
612 #if $source.ref_source=="history":
613 --genome $source.input1
614 #else:
615 --genome '$source.input1_2bit.fields.path'
616 #end if
617 </token>
618
619 <xml name="effectiveGenomeSize">
620 <conditional name="effectiveGenomeSize">
621 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
622 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.
623 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
624 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
625 <option value="93260000">ce10 (93260000)</option>
626 <option value="130428560">dm3 (130428560)</option>
627 <option value="125464728">dm6 (125464728)</option>
628 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
629 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
630 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
631 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
632 <option value="specific">user specified</option>
633 </param>
634 <when value="specific">
635 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
636 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
637 </when>
638 <when value="93260000" />
639 <when value="130428560" />
640 <when value="125464728" />
641 <when value="2685511504" />
642 <when value="2701495761" />
643 <when value="2304947926" />
644 <when value="2308125349" />
645 </conditional>
646 </xml>
647
648 <xml name="skipNAs">
649 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
650 label="Ignore missing data?"
651 help="This parameter determines if non-covered regions
652 (regions without overlapping reads) in a bam/bigWig file
653 should be skipped. The default is to treat those
654 regions as having a value of zero. The decision to
655 skip non-covered regions depends on the interpretation
656 of the data. Non-covered regions may represent, for
657 example, repetitive regions that should be ignored.
658 (default: False)" />
659 </xml>
660
661 <xml name="skipZeroOverZero">
662 <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
663 help="Skip bins where BOTH files lack coverage.">
664 <option value="" selected="true">No</option>
665 <option value="--skipZeroOverZero">Yes, skip them.</option>
666 </param>
667 </xml>
668
669 <xml name="exactScaling">
670 <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
671 label="Compute an exact scaling factor"
672 help="Compute an exact scaling factor rather than one based on
673 sampled reads. This is only useful in cases where you are
674 filtering some alignments out AND this are both rare and
675 tend to clump together in the genome. In such cases the
676 region-based sampling employed by deepTools would produce
677 inaccurate scaling factors. Note that this option results
678 in the process taking significantly more time to complete." />
679 </xml>
680
681 <xml name="input_save_matrix_values">
682 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
683 </xml>
684
685 <xml name="input_graphic_output_settings">
686 <conditional name="output" >
687 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
688 <option value="no" selected="true">no</option>
689 <option value="yes">yes</option>
690 </param>
691 <when value="no" />
692 <when value="yes">
693 <yield />
694 <param name="saveSortedRegions" type="boolean"
695 argument="--outFileSortedRegions"
696 label="Save the regions after skipping zeros or min/max threshold values"
697 help="The order of the regions in the file follows the sorting order selected. This is useful,
698 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
699 </when>
700 </conditional>
701 </xml>
702
703
704 <xml name="input_image_file_format">
705 <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">
706 <option value="png" selected="true">png</option>
707 <option value="pdf">pdf</option>
708 <option value="svg">svg</option>
709 <option value="eps">eps</option>
710 <option value="plotly">plotly</option>
711 </param>
712 </xml>
713
714 <xml name="output_dpi">
715 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
716 label="Image dpi" help=""/>
717 </xml>
718
719 <xml name="output_image_file_format">
720 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
721 <change_format>
722 <when input="output.outFileFormat" value="pdf" format="pdf" />
723 <when input="output.outFileFormat" value="svg" format="svg" />
724 <when input="output.outFileFormat" value="eps" format="eps" />
725 <when input="output.outFileFormat" value="plotly" format="html" />
726 </change_format>
727 </data>
728 </xml>
729
730 <xml name="output_image_file_format_not_nested">
731 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
732 <change_format>
733 <when input="outFileFormat" value="pdf" format="pdf" />
734 <when input="outFileFormat" value="svg" format="svg" />
735 <when input="outFileFormat" value="eps" format="eps" />
736 <when input="outFileFormat" value="plotly" format="html" />
737 </change_format>
738 </data>
739 </xml>
740
741 <xml name="output_save_matrix_values">
742 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
743 <filter>
744 ((
745 output['showOutputSettings'] == 'yes' and
746 output['saveMatrix'] is True
747 ))
748 </filter>
749 </data>
750 </xml>
751
752 <xml name="output_graphic_outputs">
753 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
754 <filter>
755 ((
756 output['showOutputSettings'] == 'yes' and
757 output['saveSortedRegions'] is True
758 ))
759 </filter>
760 </data>
761 </xml>
762
763 <xml name="colorMap">
764 <param name="colorMap" type="select" label="Color map to use for the heatmap"
765 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
766 <option value="RdYlBu" selected="true">RdYlBu</option>
767 <option value="Accent">Accent</option>
768 <option value="Spectral">Spectral</option>
769 <option value="Set1">Set1</option>
770 <option value="Set2">Set2</option>
771 <option value="Set3">Set3</option>
772 <option value="Dark2">Dark2</option>
773 <option value="Reds">Reds</option>
774 <option value="Oranges">Oranges</option>
775 <option value="Greens">Greens</option>
776 <option value="Blues">Blues</option>
777 <option value="Greys">Greys</option>
778 <option value="Purples">Purples</option>
779 <option value="Paired">Paired</option>
780 <option value="Pastel1">Pastel1</option>
781 <option value="Pastel2">Pastel2</option>
782 <option value="spring">spring</option>
783 <option value="summer">summer</option>
784 <option value="autumn">autumn</option>
785 <option value="winter">winter</option>
786 <option value="hot">hot</option>
787 <option value="coolwarm">coolwarm</option>
788 <option value="cool">cool</option>
789 <option value="seismic">seismic</option>
790 <option value="terrain">terrain</option>
791 <option value="ocean">ocean</option>
792 <option value="rainbow">rainbow</option>
793 <option value="bone">bone</option>
794 <option value="flag">flag</option>
795 <option value="prism">prism</option>
796 <option value="cubehelix">cubehelix</option>
797 <option value="binary">binary</option>
798 <option value="pink">pink</option>
799 <option value="gray">gray</option>
800 <option value="copper">copper</option>
801 <option value="BrBG">BrBG</option>
802 <option value="BuGn">BuGn</option>
803 <option value="BuPu">BuPu</option>
804 <option value="GnBu">GnBu</option>
805 <option value="OrRd">OrRd</option>
806 <option value="PiYG">PiYG</option>
807 <option value="PRGn">PRGn</option>
808 <option value="PuOr">PuOr</option>
809 <option value="PuRd">PuRd</option>
810 <option value="PuBu">PuBu</option>
811 <option value="RdBu">RdBu</option>
812 <option value="RdGy">RdGy</option>
813 <option value="RdPu">RdPu</option>
814 <option value="YlGn">YlGn</option>
815 <option value="PuBuGn">PuBuGn</option>
816 <option value="RdYlGn">RdYlGn</option>
817 <option value="YlGnBu">YlGnBu</option>
818 <option value="YlOrBr">YlOrBr</option>
819 <option value="YlOrRd">YlOrRd</option>
820 <option value="gist_gray">gist_gray</option>
821 <option value="gist_stern">gist_stern</option>
822 <option value="gist_earth">gist_earth</option>
823 <option value="gist_yarg">gist_yarg</option>
824 <option value="gist_ncar">gist_ncar</option>
825 <option value="gist_rainbow">gist_rainbow</option>
826 <option value="gist_heat">gist_heat</option>
827 <option value="gnuplot">gnuplot</option>
828 <option value="gnuplot2">gnuplot2</option>
829 <option value="CMRmap">CMRmap</option>
830 <option value="bwr">bwr</option>
831 <option value="hsv">hsv</option>
832 <option value="brg">brg</option>
833 <option value="jet">jet</option>
834 <option value="afmhot">afmhot</option>
835 <option value="Wistia">Wistia</option>
836 <option value="cividis">cividis</option>
837 <option value="icefire">icefire</option>
838 <option value="inferno">inferno</option>
839 <option value="magma">magma</option>
840 <option value="mako">mako</option>
841 <option value="nipy_spectral">nipy_spectral</option>
842 <option value="plasma">plasma</option>
843 <option value="rocket">rocket</option>
844 <option value="tab10">tab10</option>
845 <option value="tab20">tab20</option>
846 <option value="tab20b">tab20b</option>
847 <option value="tab20c">tab20c</option>
848 <option value="twilight">twilight</option>
849 <option value="twilight_shifted">twilight_shifted</option>
850 <option value="viridis">viridis</option>
851 <option value="vlag">vlag</option>
852 <option value="Accent_r">Accent reversed</option>
853 <option value="Spectral_r">Spectral reversed</option>
854 <option value="Set1_r">Set1 reversed</option>
855 <option value="Set2_r">Set2 reversed</option>
856 <option value="Set3_r">Set3 reversed</option>
857 <option value="Dark2_r">Dark2 reversed</option>
858 <option value="Reds_r">Reds reversed</option>
859 <option value="Oranges_r">Oranges reversed</option>
860 <option value="Greens_r">Greens reversed</option>
861 <option value="Blues_r">Blues reversed</option>
862 <option value="Greys_r">Greys reversed</option>
863 <option value="Purples_r">Purples reversed</option>
864 <option value="Paired_r">Paired reversed</option>
865 <option value="Pastel1_r">Pastel1 reversed</option>
866 <option value="Pastel2_r">Pastel2 reversed</option>
867 <option value="spring_r">spring reversed</option>
868 <option value="summer_r">summer reversed</option>
869 <option value="autumn_r">autumn reversed</option>
870 <option value="winter_r">winter reversed</option>
871 <option value="hot_r">hot reversed</option>
872 <option value="coolwarm_r">coolwarm reversed</option>
873 <option value="cool_r">cool reversed</option>
874 <option value="seismic_r">seismic reversed</option>
875 <option value="terrain_r">terrain reversed</option>
876 <option value="ocean_r">ocean reversed</option>
877 <option value="rainbow_r">rainbow reversed</option>
878 <option value="bone_r">bone reversed</option>
879 <option value="flag_r">flag reversed</option>
880 <option value="prism_r">prism reversed</option>
881 <option value="cubehelix_r">cubehelix reversed</option>
882 <option value="binary_r">binary reversed</option>
883 <option value="pink_r">pink reversed</option>
884 <option value="gray_r">gray reversed</option>
885 <option value="copper_r">copper reversed</option>
886 <option value="BrBG_r">BrBG reversed</option>
887 <option value="BuGn_r">BuGn reversed</option>
888 <option value="BuPu_r">BuPu reversed</option>
889 <option value="GnBu_r">GnBu reversed</option>
890 <option value="OrRd_r">OrRd reversed</option>
891 <option value="PiYG_r">PiYG reversed</option>
892 <option value="PRGn_r">PRGn reversed</option>
893 <option value="PuOr_r">PuOr reversed</option>
894 <option value="PuRd_r">PuRd reversed</option>
895 <option value="PuBu_r">PuBu reversed</option>
896 <option value="RdBu_r">RdBu reversed</option>
897 <option value="RdGy_r">RdGy reversed</option>
898 <option value="RdPu_r">RdPu reversed</option>
899 <option value="YlGn_r">YlGn reversed</option>
900 <option value="PuBuGn_r">PuBuGn reversed</option>
901 <option value="RdYlBu_r">RdYlBu reversed</option>
902 <option value="RdYlGn_r">RdYlGn reversed</option>
903 <option value="YlGnBu_r">YlGnBu reversed</option>
904 <option value="YlOrBr_r">YlOrBr reversed</option>
905 <option value="YlOrRd_r">YlOrRd reversed</option>
906 <option value="gist_gray_r">gist_gray reversed</option>
907 <option value="gist_stern_r">gist_stern reversed</option>
908 <option value="gist_earth_r">gist_earth reversed</option>
909 <option value="gist_yarg_r">gist_yarg reversed</option>
910 <option value="gist_ncar_r">gist_ncar reversed</option>
911 <option value="gist_rainbow_r">gist_rainbow reversed</option>
912 <option value="gist_heat_r">gist_heat reversed</option>
913 <option value="gnuplot_r">gnuplot reversed</option>
914 <option value="gnuplot2_r">gnuplot2 reversed</option>
915 <option value="CMRmap_r">CMRmap reversed</option>
916 <option value="bwr_r">bwr reversed</option>
917 <option value="hsv_r">hsv reversed</option>
918 <option value="brg_r">brg reversed</option>
919 <option value="jet_r">jet reversed</option>
920 <option value="afmhot_r">afmhot reversed</option>
921 <option value="Wistia_r">Wistia reversed</option>
922 <option value="cividis_r">cividis reversed</option>
923 <option value="icefire_r">icefire reversed</option>
924 <option value="inferno_r">inferno reversed</option>
925 <option value="magma_r">magma reversed</option>
926 <option value="mako_r">mako reversed</option>
927 <option value="nipy_spectral_r">nipy_spectral reversed</option>
928 <option value="plasma_r">plasma reversed</option>
929 <option value="rocket_r">rocket reversed</option>
930 <option value="tab10_r">tab10 reversed</option>
931 <option value="tab20_r">tab20 reversed</option>
932 <option value="tab20b_r">tab20b reversed</option>
933 <option value="tab20c_r">tab20c reversed</option>
934 <option value="twilight_r">twilight reversed</option>
935 <option value="twilight_shifted_r">twilight_shifted reversed</option>
936 <option value="viridis_r">viridis reversed</option>
937 <option value="vlag_r">vlag reversed</option>
938 </param>
939
940 </xml>
941
942 </macros>