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comparison deepTools_macros.xml @ 0:1638c02b28b5 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
author bgruening
date Mon, 05 Dec 2016 08:09:05 -0500
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children 0240a81c3ae6
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-1:000000000000 0:1638c02b28b5
1 <macros>
2
3 <xml name="advancedOpt_scaffold">
4 <conditional name="advancedOpt">
5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
6 <option value="no" selected="true">no</option>
7 <option value="yes">yes</option>
8 </param>
9 <when value="no" />
10 <when value="yes">
11 <yield/>
12 </when>
13 </conditional>
14 </xml>
15
16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
20 --extendReads
21 #end if
22 $advancedOpt.ignoreDuplicates
23 $advancedOpt.centerReads
24 #if $advancedOpt.minMappingQuality:
25 --minMappingQuality '$advancedOpt.minMappingQuality'
26 #end if
27 #if $advancedOpt.samFlagInclude:
28 --samFlagInclude $advancedOpt.samFlagInclude
29 #end if
30 #if $advancedOpt.samFlagExclude:
31 --samFlagExclude $advancedOpt.samFlagExclude
32 #end if
33 #if $advancedOpt.minFragmentLength:
34 --minFragmentLength $advancedOpt.minFragmentLength
35 #end if
36 #if $advancedOpt.maxFragmentLength:
37 --maxFragmentLength $advancedOpt.maxFragmentLength
38 #end if
39 </token>
40
41 <token name="@ADVANCED_OPTS_GTF@">
42 $advancedOpt.metagene
43 #if $advancedOpt.transcriptID:
44 --transcriptID $advancedOpt.transcriptID
45 #end if
46 #if $advancedOpt.exonID:
47 --exonID $advancedOpt.exonID
48 #end if
49 #if $advancedOpt.transcript_id_designator:
50 --transcript_id_designator $advancedOpt.transcript_id_designator
51 #end if
52 </token>
53
54 <xml name="heatmap_options">
55 <expand macro="zMin_zMax" />
56 <expand macro="colorMap" />
57 <expand macro="plotTitle" />
58 <expand macro="plotNumbers" />
59 </xml>
60
61 <token name="@HEATMAP_OPTIONS@">
62 #if str($plotting_type.zMin) != "":
63 --zMin $plotting_type.zMin
64 #end if
65 #if str($plotting_type.zMax) != "":
66 --zMax $plotting_type.zMax
67 #end if
68 --colorMap '$plotting_type.colorMap'
69 $plotting_type.plotNumbers
70 --plotTitle '$plotting_type.plotTitle'
71 </token>
72
73
74 <xml name="includeZeros">
75 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
76 label="Include zeros"
77 help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
78 </xml>
79
80 <xml name="zMin_zMax">
81 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
82 help="If not specified the value is set automatically."/>
83 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
84 help="If not specified the value is set automatically."/>
85 </xml>
86
87 <xml name="region_limit_operation">
88 <param argument="--region" type="text" value=""
89 label="Region of the genome to limit the operation to"
90 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;.">
91 <sanitizer>
92 <valid initial="string.letters,string.digits">
93 <add value="|"/>
94 <add value=":"/>
95 </valid>
96 </sanitizer>
97 </param>
98 </xml>
99
100 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
101 <token name="@WRAPPER_VERSION@">2.4.1</token>
102 <xml name="requirements">
103 <requirements>
104 <requirement type="package" version="2.7.10">python</requirement>
105 <requirement type="package" version="2.4.1">deeptools</requirement>
106 <yield />
107 </requirements>
108 <expand macro="stdio" />
109 <version_command>@BINARY@ --version</version_command>
110 </xml>
111
112 <xml name="smoothLength">
113 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
114 label="Smooth values using the following length (in bases)"
115 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."/>
116 </xml>
117
118
119 <xml name="kmeans_clustering">
120 <conditional name="used_multiple_regions">
121 <param name="used_multiple_regions_options" type="select"
122 label="Did you compute the matrix with more than one groups of regions?"
123 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.">
124 <option value="yes">Yes, I used multiple groups of regions</option>
125 <option value="no">No, I used only one group</option>
126 </param>
127 <when value="no">
128 <conditional name="clustering">
129 <param name="clustering_options" type="select" label="Clustering algorithm">
130 <option value="none">No clustering</option>
131 <option value="kmeans">Kmeans clustering</option>
132 <option value="hclust">Hierarchical clustering</option>
133 </param>
134 <when value="kmeans">
135 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
136 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
137 This only works for data that is not grouped, otherwise only the first group will be clustered.
138 If more specific clustering methods are required it is advisable to save the underlying matrix and
139 run the clustering using other software."/>
140 </when>
141 <when value="hclust">
142 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
143 help="WARNING: This option causes the tool to run for a very long time! When this option is
144 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
145 This only works for data that is not grouped, otherwise only the first group will be clustered.
146 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
147 If more specific clustering methods are required it is advisable to save the underlying matrix and
148 run the clustering using other software."/>
149 </when>
150 <when value="none" />
151 </conditional>
152 </when>
153 <when value="yes" />
154 </conditional>
155 </xml>
156
157 <token name="@KMEANS_CLUSTERING@">
158 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
159 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
160 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
161 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
162 #end if
163 #end if
164 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
165 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
166 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
167 #end if
168 #end if
169 #end if
170 </token>
171
172 <xml name="samFlags">
173 <param argument="--samFlagInclude" type="integer" optional="True" value=""
174 label="Include reads based on the SAM flag"
175 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."/>
176 <param argument="--samFlagExclude" type="integer" optional="True" value=""
177 label="Exclude reads based on the SAM flag"
178 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."/>
179 </xml>
180
181 <xml name="fragLength">
182 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
183 label="Minimum fragment length for inclusion."
184 help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
185 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
186 label="Maximum fragment length for inclusion."
187 help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
188 </xml>
189
190 <xml name="read_processing_options">
191 <expand macro="extendReads" />
192 <expand macro="ignoreDuplicates" />
193 <expand macro="centerReads" />
194 <expand macro="minMappingQuality" />
195 <expand macro="samFlags" />
196 <expand macro="fragLength" />
197 </xml>
198
199 <xml name="gtf_options">
200 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
201 label="Use a metagene model"
202 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." />
203 <param argument="--transcriptID" optional="True" value="transcript" type="text"
204 label="trascript designator"
205 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" />
206 <param argument="--exonID" optional="True" value="exon" type="text"
207 label="exon designator"
208 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" />
209 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
210 label="transcriptID key designator"
211 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
212 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
213 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
214 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
215 </xml>
216
217
218 <xml name="plotNumbers">
219 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
220 label="Plot the correlation value"
221 help="If set, then the correlation number is plotted on top of the heatmap."/>
222 </xml>
223
224 <xml name="extendReads">
225 <conditional name="doExtendCustom">
226 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
227 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
228 By default *each* read mate is extended.
229 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
230 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
231 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
232 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
233 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
234 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
235 <option value="custom">A custom length, which will be applied to ALL reads.</option>
236 </param>
237 <when value="no" />
238 <when value="yes" />
239 <when value="custom">
240 <param name="extendReadsValue" type="integer" value="300" min="1"
241 label="Extend reads to the given average fragment size"
242 help="Extend all reads to this length" />
243 </when>
244 </conditional>
245 </xml>
246
247 <xml name="corMethod">
248 <param argument="--corMethod" type="select" label="Correlation method">
249 <option value="spearman" selected="True">Spearman</option>
250 <option value="pearson">Pearson</option>
251 </param>
252 </xml>
253
254 <xml name="distanceBetweenBins">
255 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
256 label="Distance between bins"
257 help="By default, multiBamSummary considers consecutive bins of
258 the specified 'Bin size'. However, to reduce the
259 computation time, a larger distance between bins can
260 be given. Larger distances result in fewer bins being
261 considered."/>
262 </xml>
263
264 <xml name="centerReads">
265 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
266 label="Center regions with respect to the fragment length"
267 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."/>
268 </xml>
269
270 <xml name="ignoreDuplicates">
271 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
272 label="Ignore duplicates"
273 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." />
274 </xml>
275
276 <xml name="sortUsing">
277 <param argument="--sortUsing" type="select" label="Method used for sorting"
278 help="For each row the method is computed.">
279 <option value="mean" selected="true">mean</option>
280 <option value="median">median</option>
281 <option value="min">min</option>
282 <option value="max">max</option>
283 <option value="sum">sum</option>
284 <option value="region_length">region length</option>
285 </param>
286 </xml>
287
288 <xml name="sortRegionsComputeMatrix">
289 <param argument="--sortRegions" type="select" label="Sort regions"
290 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
291 <option value="no">no ordering</option>
292 <option value="keep" selected="true">maintain the same ordering as the input files</option>
293 <option value="descend">descending order</option>
294 <option value="ascend">ascending order</option>
295 </param>
296 </xml>
297
298 <xml name="sortRegions">
299 <param argument="--sortRegions" type="select" label="Sort regions"
300 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
301 <option value="no">no ordering</option>
302 <option value="descend">descending order</option>
303 <option value="ascend">ascending order</option>
304 </param>
305 </xml>
306
307 <xml name="minMappingQuality">
308 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
309 label="Minimum mapping quality"
310 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
311 </xml>
312
313 <xml name="skipZeros">
314 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
315 label ="Skip zeros"
316 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />
317 </xml>
318
319 <xml name="fragmentLength">
320 <param argument="--fragmentLength" type="integer" value="300" min="1"
321 label="Fragment length used for the sequencing"
322 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
323 </xml>
324
325 <xml name="scaleFactor">
326 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
327 help="When used in combination with --normalizeTo1x or
328 --normalizeUsingRPKM, the computed scaling factor will
329 be multiplied by the given scale factor." />
330 </xml>
331
332 <xml name="scaleFactors">
333 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
334 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
335 </xml>
336
337 <xml name="stdio">
338 <stdio>
339 <exit_code range="1:" />
340 <exit_code range=":-1" />
341 <regex match="Error:" />
342 <regex match="Exception:" />
343 <regex match="EXception:" />
344 <regex match="Traceback" />
345 </stdio>
346 </xml>
347
348 <xml name="pseudocount">
349 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
350 </xml>
351
352 <token name="@REFERENCES@">
353
354 .. class:: infomark
355
356 For more information on the tools, please visit our `help site`_.
357
358 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
359
360 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
361
362 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
363 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
364 .. _help site: https://deeptools.readthedocs.org/
365
366 </token>
367 <xml name="citations">
368 <citations>
369 <citation type="doi">10.1093/nar/gkw257</citation>
370 <yield />
371 </citations>
372 </xml>
373
374 <xml name="multiple_input_bams">
375 <conditional name="multibam_conditional">
376 <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.">
377 <option value="No" selected="true">No</option>
378 <option value="Yes">Yes</option>
379 </param>
380 <when value="No">
381 <param argument="--bamfiles" type="data" format="bam" min="1"
382 label="Bam file" multiple="true"
383 help=""/>
384 </when>
385 <when value="Yes">
386 <repeat name="multibam_repeats" min="1" title="BAM Files">
387 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
388 </repeat>
389 </when>
390 </conditional>
391 </xml>
392
393 <xml name="multiple_input_bams_min2">
394 <conditional name="multibam_conditional">
395 <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
396 is vital to you, select Yes below.">
397 <option value="No" selected="true">No</option>
398 <option value="Yes">Yes</option>
399 </param>
400 <when value="No">
401 <param argument="--bamfiles" type="data" format="bam" min="2"
402 label="Bam file" multiple="true"
403 help=""/>
404 </when>
405 <when value="Yes">
406 <repeat name="multibam_repeats" min="2" title="BAM Files">
407 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
408 </repeat>
409 </when>
410 </conditional>
411 </xml>
412
413 <xml name="multiple_input_bigwigs">
414 <conditional name="multibigwig_conditional">
415 <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
416 is vital to you, select Yes below.">
417 <option value="No" selected="true">No</option>
418 <option value="Yes">Yes</option>
419 </param>
420 <when value="No">
421 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
422 label="Bigwig file"
423 help="A Bigwig file."/>
424 </when>
425 <when value="Yes">
426 <repeat name="multibigwig_repeats" min="2" title="BigWig files">
427 <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
428 </repeat>
429 </when>
430 </conditional>
431 </xml>
432
433 <xml name="plotTitle">
434 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
435 label="Title of the plot"
436 help="Title of the plot, to be printed on top of the generated image." />
437 </xml>
438
439
440 <token name="@multiple_input_bams@">
441 <![CDATA[
442 #set files=[]
443 #set labels=[]
444 #if $multibam_conditional.orderMatters == "No":
445 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
446 ln -s "${bamfile}" "./${counter}.bam" &&
447 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
448 #silent $files.append('%s.bam' % $counter)
449 #silent $labels.append("'%s'" % ($bamfile.display_name))
450 #end for
451 #else:
452 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
453 ln -s "${f.bamfile}" "./${counter}.bam" &&
454 ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
455 #silent $files.append('%s.bam' % $counter)
456 #silent $labels.append("'%s'" % ($f.bamfile.display_name))
457 #end for
458 #end if
459 ]]>
460 </token>
461
462 <token name="@multiple_input_bigwigs@">
463 <![CDATA[
464 #set files=[]
465 #set labels=[]
466 #if $multibigwig_conditional.orderMatters == "No":
467 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
468 ln -s "${bigwig}" "${counter}.bw" &&
469 #silent $files.append('%s.bw' % $counter)
470 #silent $labels.append("'%s'" % ($bigwig.display_name))
471 #end for
472 #else:
473 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
474 ln -s "${f.bigwig}" "${counter}.bw" &&
475 #silent $files.append('%s.bw' % $counter)
476 #silent $labels.append("'%s'" % ($f.bigwig.display_name))
477 #end for
478 #end if
479 ]]>
480 </token>
481
482 <xml name="blacklist">
483 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
484 label="Blacklisted regions in BED/GTF format"
485 help="One or more files containing regions to exclude from the analysis" />
486 </xml>
487
488 <token name="@blacklist@">
489 <![CDATA[
490 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
491 #set blfiles=[]
492 #for $f in $advancedOpt.blackListFileName:
493 #silent $blfiles.append("'%s'" % $f)
494 #end for
495 #if $blfiles != ["'None'"]:
496 --blackListFileName #echo ' '.join($blfiles)#
497 #end if
498 #end if
499 ]]>
500 </token>
501
502 <xml name="multiple_bed">
503 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
504 label="Regions in BED/GTF format"
505 help="One or more files containing regions to include in the analysis" />
506 </xml>
507
508 <token name="@multiple_bed@">
509 <![CDATA[
510 #set files=[]
511 #set labels=[]
512 #for $f in $BED:
513 #silent $files.append("'%s'" % $f)
514 #silent $labels.append("'%s'" % $f.display_name)
515 #end for
516 #if len($files) > 0:
517 --BED #echo ' '.join($files)#
518 --regionLabels #echo ' '.join($labels)#
519 #end if
520 ]]>
521 </token>
522
523 <xml name="reference_genome_source">
524 <conditional name="source">
525 <param name="ref_source" type="select" label="Reference genome">
526 <option value="cached">locally cached</option>
527 <option value="history">in your history</option>
528 </param>
529 <when value="cached">
530 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
531 <options from_data_table="lastz_seqs">
532 <filter type="sort_by" column="1" />
533 <validator type="no_options" message="No indexes are available." />
534 </options>
535 </param>
536 </when>
537 <when value="history">
538 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
539 </when>
540 </conditional>
541 </xml>
542
543 <token name="@reference_genome_source@">
544 #if $source.ref_source=="history":
545 --genome $source.input1
546 #else:
547 --genome "$source.input1_2bit.fields.path"
548 #end if
549 </token>
550
551 <xml name="effectiveGenomeSize">
552 <conditional name="effectiveGenomeSize">
553 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
554 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.
555 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
556 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.">
557 <option value="93260000">ce10 (93260000)</option>
558 <option value="121400000">dm3 (121400000)</option>
559 <option value="2451960000" selected="true">hg19 (2451960000)</option>
560 <option value="2150570000">mm9 (2150570000)</option>
561 <option value="specific">user specified</option>
562 </param>
563 <when value="specific">
564 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
565 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
566 </when>
567 <when value="2150570000" />
568 <when value="2451960000" />
569 <when value="121400000" />
570 <when value="93260000" />
571 </conditional>
572 </xml>
573
574 <xml name="skipNAs">
575 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
576 label="Ignore missing data?"
577 help="This parameter determines if non-covered regions
578 (regions without overlapping reads) in a bam/bigWig file
579 should be skipped. The default is to treat those
580 regions as having a value of zero. The decision to
581 skip non-covered regions depends on the interpretation
582 of the data. Non-covered regions may represent, for
583 example, repetitive regions that should be ignored.
584 (default: False)" />
585 </xml>
586
587 <xml name="input_save_matrix_values">
588 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
589 </xml>
590
591 <xml name="input_graphic_output_settings">
592 <conditional name="output" >
593 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
594 <option value="no" selected="true">no</option>
595 <option value="yes">yes</option>
596 </param>
597 <when value="no" />
598 <when value="yes">
599 <yield />
600 <param name="saveSortedRegions" type="boolean"
601 label="Save the regions after skipping zeros or min/max threshold values"
602 help="The order of the regions in the file follows the sorting order selected. This is useful,
603 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
604 </when>
605 </conditional>
606 </xml>
607
608
609 <xml name="input_image_file_format">
610 <param argument="--outFileFormat" type="select" label="Image file format">
611 <option value="png" selected="true">png</option>
612 <option value="pdf">pdf</option>
613 <option value="svg">svg</option>
614 <option value="eps">eps</option>
615 </param>
616 </xml>
617
618 <xml name="output_dpi">
619 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
620 label="Image dpi" help=""/>
621 </xml>
622
623 <xml name="output_image_file_format">
624 <data format="png" name="outFileName" label="${tool.name} image">
625 <change_format>
626 <when input="output.outFileFormat" value="pdf" format="pdf" />
627 <when input="output.outFileFormat" value="svg" format="svg" />
628 <when input="output.outFileFormat" value="eps" format="eps" />
629 </change_format>
630 </data>
631 </xml>
632
633 <xml name="output_image_file_format_not_nested">
634 <data format="png" name="outFileName" label="${tool.name} image">
635 <change_format>
636 <when input="outFileFormat" value="pdf" format="pdf" />
637 <when input="outFileFormat" value="svg" format="svg" />
638 <when input="outFileFormat" value="eps" format="eps" />
639 </change_format>
640 </data>
641 </xml>
642
643 <xml name="output_save_matrix_values">
644 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
645 <filter>
646 ((
647 output['showOutputSettings'] == 'yes' and
648 output['saveMatrix'] is True
649 ))
650 </filter>
651 </data>
652 </xml>
653
654 <xml name="output_graphic_outputs">
655 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
656 <filter>
657 ((
658 output['showOutputSettings'] == 'yes' and
659 output['saveSortedRegions'] is True
660 ))
661 </filter>
662 </data>
663 </xml>
664
665 <xml name="colorMap">
666 <param name="colorMap" type="select" label="Color map to use for the heatmap"
667 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
668 multiple="true">
669 <option value="RdYlBu" selected="true">RdYlBu</option>
670 <option value="Accent">Accent</option>
671 <option value="Spectral">Spectral</option>
672 <option value="Set1">Set1</option>
673 <option value="Set2">Set2</option>
674 <option value="Set3">Set3</option>
675 <option value="Dark2">Dark2</option>
676 <option value="Reds">Reds</option>
677 <option value="Oranges">Oranges</option>
678 <option value="Greens">Greens</option>
679 <option value="Blues">Blues</option>
680 <option value="Greys">Greys</option>
681 <option value="Purples">Purples</option>
682 <option value="Paired">Paired</option>
683 <option value="Pastel1">Pastel1</option>
684 <option value="Pastel2">Pastel2</option>
685 <option value="spring">spring</option>
686 <option value="summer">summer</option>
687 <option value="autumn">autumn</option>
688 <option value="winter">winter</option>
689 <option value="hot">hot</option>
690 <option value="coolwarm">coolwarm</option>
691 <option value="cool">cool</option>
692 <option value="seismic">seismic</option>
693 <option value="terrain">terrain</option>
694 <option value="ocean">ocean</option>
695 <option value="rainbow">rainbow</option>
696 <option value="bone">bone</option>
697 <option value="flag">flag</option>
698 <option value="prism">prism</option>
699 <option value="cubehelix">cubehelix</option>
700 <option value="binary">binary</option>
701 <option value="pink">pink</option>
702 <option value="gray">gray</option>
703 <option value="copper">copper</option>
704 <option value="BrBG">BrBG</option>
705 <option value="BuGn">BuGn</option>
706 <option value="BuPu">BuPu</option>
707 <option value="GnBu">GnBu</option>
708 <option value="OrRd">OrRd</option>
709 <option value="PiYG">PiYG</option>
710 <option value="PRGn">PRGn</option>
711 <option value="PuOr">PuOr</option>
712 <option value="PuRd">PuRd</option>
713 <option value="PuBu">PuBu</option>
714 <option value="RdBu">RdBu</option>
715 <option value="RdGy">RdGy</option>
716 <option value="RdPu">RdPu</option>
717 <option value="YlGn">YlGn</option>
718 <option value="PuBuGn">PuBuGn</option>
719 <option value="RdYlGn">RdYlGn</option>
720 <option value="YlGnBu">YlGnBu</option>
721 <option value="YlOrBr">YlOrBr</option>
722 <option value="YlOrRd">YlOrRd</option>
723 <option value="gist_gray">gist_gray</option>
724 <option value="gist_stern">gist_stern</option>
725 <option value="gist_earth">gist_earth</option>
726 <option value="gist_yarg">gist_yarg</option>
727 <option value="gist_ncar">gist_ncar</option>
728 <option value="gist_rainbow">gist_rainbow</option>
729 <option value="gist_heat">gist_heat</option>
730 <option value="gnuplot">gnuplot</option>
731 <option value="gnuplot2">gnuplot2</option>
732 <option value="CMRmap">CMRmap</option>
733 <option value="bwr">bwr</option>
734 <option value="hsv">hsv</option>
735 <option value="brg">brg</option>
736 <option value="jet">jet</option>
737 <option value="afmhot">afmhot</option>
738 <option value="Accent_r">Accent reversed</option>
739 <option value="Spectral_r">Spectral reversed</option>
740 <option value="Set1_r">Set1 reversed</option>
741 <option value="Set2_r">Set2 reversed</option>
742 <option value="Set3_r">Set3 reversed</option>
743 <option value="Dark2_r">Dark2 reversed</option>
744 <option value="Reds_r">Reds reversed</option>
745 <option value="Oranges_r">Oranges reversed</option>
746 <option value="Greens_r">Greens reversed</option>
747 <option value="Blues_r">Blues reversed</option>
748 <option value="Greys_r">Greys reversed</option>
749 <option value="Purples_r">Purples reversed</option>
750 <option value="Paired_r">Paired reversed</option>
751 <option value="Pastel1_r">Pastel1 reversed</option>
752 <option value="Pastel2_r">Pastel2 reversed</option>
753 <option value="spring_r">spring reversed</option>
754 <option value="summer_r">summer reversed</option>
755 <option value="autumn_r">autumn reversed</option>
756 <option value="winter_r">winter reversed</option>
757 <option value="hot_r">hot reversed</option>
758 <option value="coolwarm_r">coolwarm reversed</option>
759 <option value="cool_r">cool reversed</option>
760 <option value="seismic_r">seismic reversed</option>
761 <option value="terrain_r">terrain reversed</option>
762 <option value="ocean_r">ocean reversed</option>
763 <option value="rainbow_r">rainbow reversed</option>
764 <option value="bone_r">bone reversed</option>
765 <option value="flag_r">flag reversed</option>
766 <option value="prism_r">prism reversed</option>
767 <option value="cubehelix_r">cubehelix reversed</option>
768 <option value="binary_r">binary reversed</option>
769 <option value="pink_r">pink reversed</option>
770 <option value="gray_r">gray reversed</option>
771 <option value="copper_r">copper reversed</option>
772 <option value="BrBG_r">BrBG reversed</option>
773 <option value="BuGn_r">BuGn reversed</option>
774 <option value="BuPu_r">BuPu reversed</option>
775 <option value="GnBu_r">GnBu reversed</option>
776 <option value="OrRd_r">OrRd reversed</option>
777 <option value="PiYG_r">PiYG reversed</option>
778 <option value="PRGn_r">PRGn reversed</option>
779 <option value="PuOr_r">PuOr reversed</option>
780 <option value="PuRd_r">PuRd reversed</option>
781 <option value="PuBu_r">PuBu reversed</option>
782 <option value="RdBu_r">RdBu reversed</option>
783 <option value="RdGy_r">RdGy reversed</option>
784 <option value="RdPu_r">RdPu reversed</option>
785 <option value="YlGn_r">YlGn reversed</option>
786 <option value="PuBuGn_r">PuBuGn reversed</option>
787 <option value="RdYlBu_r">RdYlBu reversed</option>
788 <option value="RdYlGn_r">RdYlGn reversed</option>
789 <option value="YlGnBu_r">YlGnBu reversed</option>
790 <option value="YlOrBr_r">YlOrBr reversed</option>
791 <option value="YlOrRd_r">YlOrRd reversed</option>
792 <option value="gist_gray_r">gist_gray reversed</option>
793 <option value="gist_stern_r">gist_stern reversed</option>
794 <option value="gist_earth_r">gist_earth reversed</option>
795 <option value="gist_yarg_r">gist_yarg reversed</option>
796 <option value="gist_ncar_r">gist_ncar reversed</option>
797 <option value="gist_rainbow_r">gist_rainbow reversed</option>
798 <option value="gist_heat_r">gist_heat reversed</option>
799 <option value="gnuplot_r">gnuplot reversed</option>
800 <option value="gnuplot2_r">gnuplot2 reversed</option>
801 <option value="CMRmap_r">CMRmap reversed</option>
802 <option value="bwr_r">bwr reversed</option>
803 <option value="hsv_r">hsv reversed</option>
804 <option value="brg_r">brg reversed</option>
805 <option value="jet_r">jet reversed</option>
806 <option value="afmhot_r">afmhot reversed</option>
807 </param>
808
809 </xml>
810
811 </macros>