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comparison deepTools_macros.xml @ 0:dfc5a344e2c2 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
author bgruening
date Thu, 15 Feb 2018 08:13:20 -0500
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children 48d08791d4f2
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-1:000000000000 0:dfc5a344e2c2
1 <macros>
2
3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
4 <token name="@WRAPPER_VERSION@">3.0.0</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="3.0.0">deeptools</requirement>
8 <requirement type="package" version="1.7">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 </valid>
122 </sanitizer>
123 </param>
124 </xml>
125
126 <xml name="smoothLength">
127 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
128 label="Smooth values using the following length (in bases)"
129 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."/>
130 </xml>
131
132
133 <xml name="kmeans_clustering">
134 <conditional name="used_multiple_regions">
135 <param name="used_multiple_regions_options" type="select"
136 label="Did you compute the matrix with more than one groups of regions?"
137 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.">
138 <option value="yes">Yes, I used multiple groups of regions</option>
139 <option value="no">No, I used only one group</option>
140 </param>
141 <when value="no">
142 <conditional name="clustering">
143 <param name="clustering_options" type="select" label="Clustering algorithm">
144 <option value="none">No clustering</option>
145 <option value="kmeans">Kmeans clustering</option>
146 <option value="hclust">Hierarchical clustering</option>
147 </param>
148 <when value="kmeans">
149 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
150 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
151 This only works for data that is not grouped, otherwise only the first group will be clustered.
152 If more specific clustering methods are required it is advisable to save the underlying matrix and
153 run the clustering using other software."/>
154 </when>
155 <when value="hclust">
156 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
157 help="WARNING: This option causes the tool to run for a very long time! When this option is
158 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
159 This only works for data that is not grouped, otherwise only the first group will be clustered.
160 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
161 If more specific clustering methods are required it is advisable to save the underlying matrix and
162 run the clustering using other software."/>
163 </when>
164 <when value="none" />
165 </conditional>
166 </when>
167 <when value="yes" />
168 </conditional>
169 </xml>
170
171 <token name="@KMEANS_CLUSTERING@">
172 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
173 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
174 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
175 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
176 #end if
177 #end if
178 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
179 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
180 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
181 #end if
182 #end if
183 #end if
184 </token>
185
186 <xml name="samFlags">
187 <param argument="--samFlagInclude" type="integer" optional="True" value=""
188 label="Include reads based on the SAM flag"
189 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."/>
190 <param argument="--samFlagExclude" type="integer" optional="True" value=""
191 label="Exclude reads based on the SAM flag"
192 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."/>
193 </xml>
194
195 <xml name="fragLength">
196 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
197 label="Minimum fragment length for inclusion."
198 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
199 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
200 label="Maximum fragment length for inclusion."
201 help="A value of 0 (the default) is equivalent to no maximum." />
202 </xml>
203
204 <xml name="read_processing_options">
205 <expand macro="extendReads" />
206 <expand macro="ignoreDuplicates" />
207 <expand macro="centerReads" />
208 <expand macro="minMappingQuality" />
209 <expand macro="samFlags" />
210 <expand macro="fragLength" />
211 </xml>
212
213 <xml name="gtf_options">
214 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
215 label="Use a metagene model"
216 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." />
217 <param argument="--transcriptID" optional="True" value="transcript" type="text"
218 label="trascript designator"
219 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
220 <param argument="--exonID" optional="True" value="exon" type="text"
221 label="exon designator"
222 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
223 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
224 label="transcriptID key designator"
225 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
226 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
227 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
228 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
229 </xml>
230
231
232 <xml name="plotNumbers">
233 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
234 label="Plot the correlation value"
235 help="If set, then the correlation number is plotted on top of the heatmap."/>
236 </xml>
237
238 <xml name="extendReads">
239 <conditional name="doExtendCustom">
240 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
241 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.
242 By default *each* read mate is extended.
243 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
244 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
245 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
246 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
247 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
248 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
249 <option value="custom">A custom length, which will be applied to ALL reads.</option>
250 </param>
251 <when value="no" />
252 <when value="yes" />
253 <when value="custom">
254 <param name="extendReadsValue" type="integer" value="300" min="1"
255 label="Extend reads to the given average fragment size"
256 help="Extend all reads to this length" />
257 </when>
258 </conditional>
259 </xml>
260
261 <xml name="corMethod">
262 <param argument="--corMethod" type="select" label="Correlation method">
263 <option value="spearman" selected="True">Spearman</option>
264 <option value="pearson">Pearson</option>
265 </param>
266 </xml>
267
268 <xml name="distanceBetweenBins">
269 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
270 label="Distance between bins"
271 help="By default, multiBamSummary considers consecutive bins of
272 the specified 'Bin size'. However, to reduce the
273 computation time, a larger distance between bins can
274 be given. Larger distances result in fewer bins being
275 considered."/>
276 </xml>
277
278 <xml name="centerReads">
279 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
280 label="Center regions with respect to the fragment length"
281 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."/>
282 </xml>
283
284 <xml name="ignoreDuplicates">
285 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
286 label="Ignore duplicates"
287 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." />
288 </xml>
289
290 <xml name="sortUsing">
291 <param argument="--sortUsing" type="select" label="Method used for sorting"
292 help="For each row the method is computed.">
293 <option value="mean" selected="true">mean</option>
294 <option value="median">median</option>
295 <option value="min">min</option>
296 <option value="max">max</option>
297 <option value="sum">sum</option>
298 <option value="region_length">region length</option>
299 </param>
300 </xml>
301
302 <xml name="sortRegionsComputeMatrix">
303 <param argument="--sortRegions" type="select" label="Sort regions"
304 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
305 <option value="no">no ordering</option>
306 <option value="keep" selected="true">maintain the same ordering as the input files</option>
307 <option value="descend">descending order</option>
308 <option value="ascend">ascending order</option>
309 </param>
310 </xml>
311
312 <xml name="sortRegions">
313 <param argument="--sortRegions" type="select" label="Sort regions"
314 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
315 <option value="no">maintain the same ordering as the input files</option>
316 <option value="descend" selected="true">descending order</option>
317 <option value="ascend">ascending order</option>
318 </param>
319 </xml>
320
321 <xml name="minMappingQuality">
322 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
323 label="Minimum mapping quality"
324 help= "If set, only reads with a mapping quality score at least this high are considered."/>
325 </xml>
326
327 <xml name="skipZeros">
328 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
329 label ="Skip zeros"
330 help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." />
331 </xml>
332
333 <xml name="fragmentLength">
334 <param argument="--fragmentLength" type="integer" min="1" optional="true"
335 label="Fragment length used for the sequencing"
336 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."/>
337 </xml>
338
339 <xml name="scaleFactor">
340 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
341 help="The computed scaling factor will be multiplied by this (default 1)." />
342 </xml>
343
344 <xml name="scaleFactors">
345 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
346 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
347 </xml>
348
349 <xml name="stdio">
350 <stdio>
351 <exit_code range="1:" />
352 <exit_code range=":-1" />
353 <regex match="Error:" />
354 <regex match="Exception:" />
355 <regex match="EXception:" />
356 <regex match="Traceback" />
357 </stdio>
358 </xml>
359
360 <xml name="pseudocount">
361 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
362 </xml>
363
364 <token name="@REFERENCES@">
365
366 .. class:: infomark
367
368 For more information on the tools, please visit our `help site`_.
369
370 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
371
372 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
373
374 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
375 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
376 .. _help site: https://deeptools.readthedocs.org/
377
378 </token>
379 <xml name="citations">
380 <citations>
381 <citation type="doi">10.1093/nar/gkw257</citation>
382 <yield />
383 </citations>
384 </xml>
385
386 <xml name="multiple_input_bams" tokens="MIN">
387 <conditional name="multibam_conditional">
388 <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.">
389 <option value="No" selected="true">No</option>
390 <option value="Yes">Yes</option>
391 </param>
392 <when value="No">
393 <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
394 label="BAM/CRAM file" multiple="true"
395 help=""/>
396 </when>
397 <when value="Yes">
398 <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
399 <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
400 </repeat>
401 </when>
402 </conditional>
403 </xml>
404
405 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
406 <conditional name="multibigwig_conditional">
407 <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
408 is vital to you, select Yes below.">
409 <option value="No" selected="true">No</option>
410 <option value="Yes">Yes</option>
411 </param>
412 <when value="No">
413 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
414 label="@LABEL@"
415 help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
416 </when>
417 <when value="Yes">
418 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
419 <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."/>
420 </repeat>
421 </when>
422 </conditional>
423 </xml>
424
425 <xml name="plotTitle">
426 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
427 label="Title of the plot"
428 help="Title of the plot, to be printed on top of the generated image." />
429 </xml>
430
431 <xml name="labelRotation">
432 <param argument="--labelRotation" type="integer" value="0"
433 label="Rotation of the X-axis labels (in degrees)"
434 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." />
435 </xml>
436
437
438 <token name="@multiple_input_bams@">
439 <![CDATA[
440 #set files=[]
441 #set labels=[]
442 #import re
443 #if $multibam_conditional.orderMatters == "No":
444 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
445 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
446 ln -s "${bamfile}" "./${counter}.bam" &&
447 #if $bamfile.ext == 'bam':
448 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
449 #else:
450 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
451 #end if
452 #silent $files.append("'%s.bam'" % $counter)
453 #silent $labels.append("'%s'" % identifier)
454 #end for
455 #else:
456 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
457 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
458 ln -s "${f.bamfiles}" "./${counter}.bam" &&
459 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
460 #if $f.bamfiles.ext == 'bam':
461 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
462 #else:
463 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
464 #end if
465 #silent $files.append("'%s.bam'" % $counter)
466 #silent $labels.append("'%s'" % $identifier)
467 #end for
468 #end if
469 ]]>
470 </token>
471
472 <token name="@multiple_input_bigwigs@">
473 <![CDATA[
474 #set files=[]
475 #set labels=[]
476 #import re
477 #if $multibigwig_conditional.orderMatters == "No":
478 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
479 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
480 ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
481 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
482 #silent $labels.append("'%s'" % $identifier)
483 #end for
484 #else:
485 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
486 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
487 ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
488 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
489 #silent $labels.append("'%s'" % $identifier)
490 #end for
491 #end if
492 ]]>
493 </token>
494
495 <xml name="blacklist">
496 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
497 label="Blacklisted regions in BED/GTF format"
498 help="One or more files containing regions to exclude from the analysis" />
499 </xml>
500
501 <token name="@blacklist@">
502 <![CDATA[
503 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
504 #set blfiles=[]
505 #for $f in $advancedOpt.blackListFileName:
506 #silent $blfiles.append("'%s'" % $f)
507 #end for
508 #if $blfiles != ["'None'"]:
509 --blackListFileName #echo ' '.join($blfiles)#
510 #end if
511 #end if
512 ]]>
513 </token>
514
515 <xml name="multiple_bed">
516 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
517 label="Regions in BED/GTF format"
518 help="One or more files containing regions to include in the analysis" />
519 </xml>
520
521 <token name="@multiple_bed@">
522 <![CDATA[
523 #set files=[]
524 #set labels=[]
525 #for $f in $BED:
526 #silent $files.append("'%s'" % $f)
527 #silent $labels.append("'%s'" % $f.display_name)
528 #end for
529 #if len($files) > 0:
530 --BED #echo ' '.join($files)#
531 --regionLabels #echo ' '.join($labels)#
532 #end if
533 ]]>
534 </token>
535
536 <xml name="reference_genome_source">
537 <conditional name="source">
538 <param name="ref_source" type="select" label="Reference genome">
539 <option value="cached">locally cached</option>
540 <option value="history">in your history</option>
541 </param>
542 <when value="cached">
543 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
544 <options from_data_table="lastz_seqs">
545 <filter type="sort_by" column="1" />
546 <validator type="no_options" message="No indexes are available." />
547 </options>
548 </param>
549 </when>
550 <when value="history">
551 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
552 </when>
553 </conditional>
554 </xml>
555
556 <token name="@reference_genome_source@">
557 #if $source.ref_source=="history":
558 --genome $source.input1
559 #else:
560 --genome "$source.input1_2bit.fields.path"
561 #end if
562 </token>
563
564 <xml name="effectiveGenomeSize">
565 <conditional name="effectiveGenomeSize">
566 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
567 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.
568 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
569 We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
570 <option value="93260000">ce10 (93260000)</option>
571 <option value="130428560">dm3 (130428560)</option>
572 <option value="125464728">dm6 (125464728)</option>
573 <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
574 <option value="2701495761">GRCh38/hg38 (2701495761)</option>
575 <option value="2304947926">GRCm37/mm9 (2304947926)</option>
576 <option value="2308125349">GRCm38/mm10 (2308125349)</option>
577 <option value="specific">user specified</option>
578 </param>
579 <when value="specific">
580 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
581 help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
582 </when>
583 <when value="93260000" />
584 <when value="130428560" />
585 <when value="125464728" />
586 <when value="2685511504" />
587 <when value="2701495761" />
588 <when value="2304947926" />
589 <when value="2308125349" />
590 </conditional>
591 </xml>
592
593 <xml name="skipNAs">
594 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
595 label="Ignore missing data?"
596 help="This parameter determines if non-covered regions
597 (regions without overlapping reads) in a bam/bigWig file
598 should be skipped. The default is to treat those
599 regions as having a value of zero. The decision to
600 skip non-covered regions depends on the interpretation
601 of the data. Non-covered regions may represent, for
602 example, repetitive regions that should be ignored.
603 (default: False)" />
604 </xml>
605
606 <xml name="input_save_matrix_values">
607 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
608 </xml>
609
610 <xml name="input_graphic_output_settings">
611 <conditional name="output" >
612 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
613 <option value="no" selected="true">no</option>
614 <option value="yes">yes</option>
615 </param>
616 <when value="no" />
617 <when value="yes">
618 <yield />
619 <param name="saveSortedRegions" type="boolean"
620 argument="--outFileSortedRegions"
621 label="Save the regions after skipping zeros or min/max threshold values"
622 help="The order of the regions in the file follows the sorting order selected. This is useful,
623 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
624 </when>
625 </conditional>
626 </xml>
627
628
629 <xml name="input_image_file_format">
630 <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.">
631 <option value="png" selected="true">png</option>
632 <option value="pdf">pdf</option>
633 <option value="svg">svg</option>
634 <option value="eps">eps</option>
635 <option value="plotly">plotly</option>
636 </param>
637 </xml>
638
639 <xml name="output_dpi">
640 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
641 label="Image dpi" help=""/>
642 </xml>
643
644 <xml name="output_image_file_format">
645 <data format="png" name="outFileName" label="${tool.name} image">
646 <change_format>
647 <when input="output.outFileFormat" value="pdf" format="pdf" />
648 <when input="output.outFileFormat" value="svg" format="svg" />
649 <when input="output.outFileFormat" value="eps" format="eps" />
650 <when input="output.outFileFormat" value="plotly" format="html" />
651 </change_format>
652 </data>
653 </xml>
654
655 <xml name="output_image_file_format_not_nested">
656 <data format="png" name="outFileName" label="${tool.name} image">
657 <change_format>
658 <when input="outFileFormat" value="pdf" format="pdf" />
659 <when input="outFileFormat" value="svg" format="svg" />
660 <when input="outFileFormat" value="eps" format="eps" />
661 <when input="outFileFormat" value="plotly" format="html" />
662 </change_format>
663 </data>
664 </xml>
665
666 <xml name="output_save_matrix_values">
667 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
668 <filter>
669 ((
670 output['showOutputSettings'] == 'yes' and
671 output['saveMatrix'] is True
672 ))
673 </filter>
674 </data>
675 </xml>
676
677 <xml name="output_graphic_outputs">
678 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
679 <filter>
680 ((
681 output['showOutputSettings'] == 'yes' and
682 output['saveSortedRegions'] is True
683 ))
684 </filter>
685 </data>
686 </xml>
687
688 <xml name="colorMap">
689 <param name="colorMap" type="select" label="Color map to use for the heatmap"
690 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
691 <option value="RdYlBu" selected="true">RdYlBu</option>
692 <option value="Accent">Accent</option>
693 <option value="Spectral">Spectral</option>
694 <option value="Set1">Set1</option>
695 <option value="Set2">Set2</option>
696 <option value="Set3">Set3</option>
697 <option value="Dark2">Dark2</option>
698 <option value="Reds">Reds</option>
699 <option value="Oranges">Oranges</option>
700 <option value="Greens">Greens</option>
701 <option value="Blues">Blues</option>
702 <option value="Greys">Greys</option>
703 <option value="Purples">Purples</option>
704 <option value="Paired">Paired</option>
705 <option value="Pastel1">Pastel1</option>
706 <option value="Pastel2">Pastel2</option>
707 <option value="spring">spring</option>
708 <option value="summer">summer</option>
709 <option value="autumn">autumn</option>
710 <option value="winter">winter</option>
711 <option value="hot">hot</option>
712 <option value="coolwarm">coolwarm</option>
713 <option value="cool">cool</option>
714 <option value="seismic">seismic</option>
715 <option value="terrain">terrain</option>
716 <option value="ocean">ocean</option>
717 <option value="rainbow">rainbow</option>
718 <option value="bone">bone</option>
719 <option value="flag">flag</option>
720 <option value="prism">prism</option>
721 <option value="cubehelix">cubehelix</option>
722 <option value="binary">binary</option>
723 <option value="pink">pink</option>
724 <option value="gray">gray</option>
725 <option value="copper">copper</option>
726 <option value="BrBG">BrBG</option>
727 <option value="BuGn">BuGn</option>
728 <option value="BuPu">BuPu</option>
729 <option value="GnBu">GnBu</option>
730 <option value="OrRd">OrRd</option>
731 <option value="PiYG">PiYG</option>
732 <option value="PRGn">PRGn</option>
733 <option value="PuOr">PuOr</option>
734 <option value="PuRd">PuRd</option>
735 <option value="PuBu">PuBu</option>
736 <option value="RdBu">RdBu</option>
737 <option value="RdGy">RdGy</option>
738 <option value="RdPu">RdPu</option>
739 <option value="YlGn">YlGn</option>
740 <option value="PuBuGn">PuBuGn</option>
741 <option value="RdYlGn">RdYlGn</option>
742 <option value="YlGnBu">YlGnBu</option>
743 <option value="YlOrBr">YlOrBr</option>
744 <option value="YlOrRd">YlOrRd</option>
745 <option value="gist_gray">gist_gray</option>
746 <option value="gist_stern">gist_stern</option>
747 <option value="gist_earth">gist_earth</option>
748 <option value="gist_yarg">gist_yarg</option>
749 <option value="gist_ncar">gist_ncar</option>
750 <option value="gist_rainbow">gist_rainbow</option>
751 <option value="gist_heat">gist_heat</option>
752 <option value="gnuplot">gnuplot</option>
753 <option value="gnuplot2">gnuplot2</option>
754 <option value="CMRmap">CMRmap</option>
755 <option value="bwr">bwr</option>
756 <option value="hsv">hsv</option>
757 <option value="brg">brg</option>
758 <option value="jet">jet</option>
759 <option value="afmhot">afmhot</option>
760 <option value="Accent_r">Accent reversed</option>
761 <option value="Spectral_r">Spectral reversed</option>
762 <option value="Set1_r">Set1 reversed</option>
763 <option value="Set2_r">Set2 reversed</option>
764 <option value="Set3_r">Set3 reversed</option>
765 <option value="Dark2_r">Dark2 reversed</option>
766 <option value="Reds_r">Reds reversed</option>
767 <option value="Oranges_r">Oranges reversed</option>
768 <option value="Greens_r">Greens reversed</option>
769 <option value="Blues_r">Blues reversed</option>
770 <option value="Greys_r">Greys reversed</option>
771 <option value="Purples_r">Purples reversed</option>
772 <option value="Paired_r">Paired reversed</option>
773 <option value="Pastel1_r">Pastel1 reversed</option>
774 <option value="Pastel2_r">Pastel2 reversed</option>
775 <option value="spring_r">spring reversed</option>
776 <option value="summer_r">summer reversed</option>
777 <option value="autumn_r">autumn reversed</option>
778 <option value="winter_r">winter reversed</option>
779 <option value="hot_r">hot reversed</option>
780 <option value="coolwarm_r">coolwarm reversed</option>
781 <option value="cool_r">cool reversed</option>
782 <option value="seismic_r">seismic reversed</option>
783 <option value="terrain_r">terrain reversed</option>
784 <option value="ocean_r">ocean reversed</option>
785 <option value="rainbow_r">rainbow reversed</option>
786 <option value="bone_r">bone reversed</option>
787 <option value="flag_r">flag reversed</option>
788 <option value="prism_r">prism reversed</option>
789 <option value="cubehelix_r">cubehelix reversed</option>
790 <option value="binary_r">binary reversed</option>
791 <option value="pink_r">pink reversed</option>
792 <option value="gray_r">gray reversed</option>
793 <option value="copper_r">copper reversed</option>
794 <option value="BrBG_r">BrBG reversed</option>
795 <option value="BuGn_r">BuGn reversed</option>
796 <option value="BuPu_r">BuPu reversed</option>
797 <option value="GnBu_r">GnBu reversed</option>
798 <option value="OrRd_r">OrRd reversed</option>
799 <option value="PiYG_r">PiYG reversed</option>
800 <option value="PRGn_r">PRGn reversed</option>
801 <option value="PuOr_r">PuOr reversed</option>
802 <option value="PuRd_r">PuRd reversed</option>
803 <option value="PuBu_r">PuBu reversed</option>
804 <option value="RdBu_r">RdBu reversed</option>
805 <option value="RdGy_r">RdGy reversed</option>
806 <option value="RdPu_r">RdPu reversed</option>
807 <option value="YlGn_r">YlGn reversed</option>
808 <option value="PuBuGn_r">PuBuGn reversed</option>
809 <option value="RdYlBu_r">RdYlBu reversed</option>
810 <option value="RdYlGn_r">RdYlGn reversed</option>
811 <option value="YlGnBu_r">YlGnBu reversed</option>
812 <option value="YlOrBr_r">YlOrBr reversed</option>
813 <option value="YlOrRd_r">YlOrRd reversed</option>
814 <option value="gist_gray_r">gist_gray reversed</option>
815 <option value="gist_stern_r">gist_stern reversed</option>
816 <option value="gist_earth_r">gist_earth reversed</option>
817 <option value="gist_yarg_r">gist_yarg reversed</option>
818 <option value="gist_ncar_r">gist_ncar reversed</option>
819 <option value="gist_rainbow_r">gist_rainbow reversed</option>
820 <option value="gist_heat_r">gist_heat reversed</option>
821 <option value="gnuplot_r">gnuplot reversed</option>
822 <option value="gnuplot2_r">gnuplot2 reversed</option>
823 <option value="CMRmap_r">CMRmap reversed</option>
824 <option value="bwr_r">bwr reversed</option>
825 <option value="hsv_r">hsv reversed</option>
826 <option value="brg_r">brg reversed</option>
827 <option value="jet_r">jet reversed</option>
828 <option value="afmhot_r">afmhot reversed</option>
829 </param>
830
831 </xml>
832
833 </macros>