Mercurial > repos > bgruening > hicexplorer_hicnormalize

comparison macros.xml @ 0:4f36f2d51d33 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:47:25 -0500
parents
children 483e507c8d42
comparison
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-1:000000000000 0:4f36f2d51d33
1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <token name="@WRAPPER_VERSION@">3.3.1</token>
4 <token name="@USE_RANGE@">
5 #if $use_range.select_use_range == "yes_use_range":
6 --range $range_min:$range_max
7 #end if
8 </token>
9
10 <xml name="requirements">
11 <requirements>
12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
13 <yield />
14 </requirements>
15 <version_command>@BINARY@ --version</version_command>
16 </xml>
17
18 <token name="@CHROMOSOME_LIST@">
19 #if $chromosome_list:
20 #set $chromosomes = []
21 #for $chrom in $chromosome_list:
22 #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
23 #end for
24 #set $chromosome_string = ' '.join($chromosomes)
25 --chromosomes $chromosome_string
26 #end if
27 </token>
28
29 <xml name="chromosome_list">
30 <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">
31 <param argument="--chromosomes" type="text" value="" >
32 <validator type="empty_field" />
33 </param>
34 </repeat>
35 </xml>
36
37 <xml name="citations">
38 <citations>
39 <citation type="doi">10.5281/zenodo.1133705</citation>
40 <yield />
41 </citations>
42 </xml>
43
44 <xml name="zMax">
45 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
46 </xml>
47 <xml name="use_range">
48 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
49 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
50 <option value="no_use_range">No restriction</option>
51 <option value="yes_use_range">Only consider counts within a range</option>
52 </param>
53 <when value="no_use_range"/>
54 <when value="yes_use_range">
55 <expand macro='range' />
56 </when>
57 </conditional>
58 </xml>
59
60 <xml name="range">
61 <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
62 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
63 </xml>
64
65 <xml name="colormap">
66 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
67 <option value="RdYlBu">RdYlBu</option>
68 <option value="Accent">Accent</option>
69 <option value="Spectral">Spectral</option>
70 <option value="Set1">Set1</option>
71 <option value="Set2">Set2</option>
72 <option value="Set3">Set3</option>
73 <option value="Dark2">Dark2</option>
74 <option value="Reds">Reds</option>
75 <option value="Oranges">Oranges</option>
76 <option value="Greens">Greens</option>
77 <option value="Blues">Blues</option>
78 <option value="Greys">Greys</option>
79 <option value="Purples">Purples</option>
80 <option value="Paired">Paired</option>
81 <option value="Pastel1">Pastel1</option>
82 <option value="Pastel2">Pastel2</option>
83 <option value="spring">spring</option>
84 <option value="summer">summer</option>
85 <option value="autumn">autumn</option>
86 <option value="winter">winter</option>
87 <option value="hot">hot</option>
88 <option value="coolwarm">coolwarm</option>
89 <option value="cool">cool</option>
90 <option value="seismic">seismic</option>
91 <option value="terrain">terrain</option>
92 <option value="ocean">ocean</option>
93 <option value="rainbow">rainbow</option>
94 <option value="bone">bone</option>
95 <option value="flag">flag</option>
96 <option value="prism">prism</option>
97 <option value="cubehelix">cubehelix</option>
98 <option value="binary">binary</option>
99 <option value="pink">pink</option>
100 <option value="gray">gray</option>
101 <option value="copper">copper</option>
102 <option value="BrBG">BrBG</option>
103 <option value="BuGn">BuGn</option>
104 <option value="BuPu">BuPu</option>
105 <option value="GnBu">GnBu</option>
106 <option value="OrRd">OrRd</option>
107 <option value="PiYG">PiYG</option>
108 <option value="PRGn">PRGn</option>
109 <option value="PuOr">PuOr</option>
110 <option value="PuRd">PuRd</option>
111 <option value="PuBu">PuBu</option>
112 <option value="RdBu">RdBu</option>
113 <option value="RdGy">RdGy</option>
114 <option value="RdPu">RdPu</option>
115 <option value="YlGn">YlGn</option>
116 <option value="PuBuGn">PuBuGn</option>
117 <option value="RdYlGn">RdYlGn</option>
118 <option value="YlGnBu">YlGnBu</option>
119 <option value="YlOrBr">YlOrBr</option>
120 <option value="YlOrRd">YlOrRd</option>
121 <option value="gist_gray">gist_gray</option>
122 <option value="gist_stern">gist_stern</option>
123 <option value="gist_earth">gist_earth</option>
124 <option value="gist_yarg">gist_yarg</option>
125 <option value="gist_ncar">gist_ncar</option>
126 <option value="gist_rainbow">gist_rainbow</option>
127 <option value="gist_heat">gist_heat</option>
128 <option value="gnuplot">gnuplot</option>
129 <option value="gnuplot2">gnuplot2</option>
130 <option value="CMRmap">CMRmap</option>
131 <option value="bwr">bwr</option>
132 <option value="hsv">hsv</option>
133 <option value="brg">brg</option>
134 <option value="jet">jet</option>
135 <option value="afmhot">afmhot</option>
136 <option value="plasma">plasma</option>
137 <option value="Accent_r">Accent reversed</option>
138 <option value="Spectral_r">Spectral reversed</option>
139 <option value="Set1_r">Set1 reversed</option>
140 <option value="Set2_r">Set2 reversed</option>
141 <option value="Set3_r">Set3 reversed</option>
142 <option value="Dark2_r">Dark2 reversed</option>
143 <option value="Reds_r">Reds reversed</option>
144 <option value="Oranges_r">Oranges reversed</option>
145 <option value="Greens_r">Greens reversed</option>
146 <option value="Blues_r">Blues reversed</option>
147 <option value="Greys_r">Greys reversed</option>
148 <option value="Purples_r">Purples reversed</option>
149 <option value="Paired_r">Paired reversed</option>
150 <option value="Pastel1_r">Pastel1 reversed</option>
151 <option value="Pastel2_r">Pastel2 reversed</option>
152 <option value="spring_r">spring reversed</option>
153 <option value="summer_r">summer reversed</option>
154 <option value="autumn_r">autumn reversed</option>
155 <option value="winter_r">winter reversed</option>
156 <option value="hot_r">hot reversed</option>
157 <option value="coolwarm_r">coolwarm reversed</option>
158 <option value="cool_r">cool reversed</option>
159 <option value="seismic_r">seismic reversed</option>
160 <option value="terrain_r">terrain reversed</option>
161 <option value="ocean_r">ocean reversed</option>
162 <option value="rainbow_r">rainbow reversed</option>
163 <option value="bone_r">bone reversed</option>
164 <option value="flag_r">flag reversed</option>
165 <option value="prism_r">prism reversed</option>
166 <option value="cubehelix_r">cubehelix reversed</option>
167 <option value="binary_r">binary reversed</option>
168 <option value="pink_r">pink reversed</option>
169 <option value="gray_r">gray reversed</option>
170 <option value="copper_r">copper reversed</option>
171 <option value="BrBG_r">BrBG reversed</option>
172 <option value="BuGn_r">BuGn reversed</option>
173 <option value="BuPu_r">BuPu reversed</option>
174 <option value="GnBu_r">GnBu reversed</option>
175 <option value="OrRd_r">OrRd reversed</option>
176 <option value="PiYG_r">PiYG reversed</option>
177 <option value="PRGn_r">PRGn reversed</option>
178 <option value="PuOr_r">PuOr reversed</option>
179 <option value="PuRd_r">PuRd reversed</option>
180 <option value="PuBu_r">PuBu reversed</option>
181 <option value="RdBu_r">RdBu reversed</option>
182 <option value="RdGy_r">RdGy reversed</option>
183 <option value="RdPu_r">RdPu reversed</option>
184 <option value="YlGn_r">YlGn reversed</option>
185 <option value="PuBuGn_r">PuBuGn reversed</option>
186 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
187 <option value="RdYlGn_r">RdYlGn reversed</option>
188 <option value="YlGnBu_r">YlGnBu reversed</option>
189 <option value="YlOrBr_r">YlOrBr reversed</option>
190 <option value="YlOrRd_r">YlOrRd reversed</option>
191 <option value="gist_gray_r">gist_gray reversed</option>
192 <option value="gist_stern_r">gist_stern reversed</option>
193 <option value="gist_earth_r">gist_earth reversed</option>
194 <option value="gist_yarg_r">gist_yarg reversed</option>
195 <option value="gist_ncar_r">gist_ncar reversed</option>
196 <option value="gist_rainbow_r">gist_rainbow reversed</option>
197 <option value="gist_heat_r">gist_heat reversed</option>
198 <option value="gnuplot_r">gnuplot reversed</option>
199 <option value="gnuplot2_r">gnuplot2 reversed</option>
200 <option value="CMRmap_r">CMRmap reversed</option>
201 <option value="bwr_r">bwr reversed</option>
202 <option value="hsv_r">hsv reversed</option>
203 <option value="brg_r">brg reversed</option>
204 <option value="jet_r">jet reversed</option>
205 <option value="afmhot_r">afmhot reversed</option>
206 <option value="plasma_r">plasma reversed</option>
207 </param>
208 </xml>
209
210 <xml name="multiple_input_matrices">
211 <repeat name="input_files" title="Hi-C Matrix files" min="2">
212 <param name="matrix" type="data" format="h5,cool"
213 label="Hi-C Matrix file"
214 help=""/>
215 <param name="mlabel" type="text" size="30" optional="true" value=""
216 label="Label"
217 help="Label to use in the output. If not given the dataset name will be used instead."/>
218 </repeat>
219 </xml>
220
221 <token name="@multiple_input_matrices@">
222 #set $matrices = []
223 #set $mlabels = []
224 #for $counter, $i in enumerate($input_files):
225 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
226 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
227
228 #if str($i.mlabel.value) != "":
229 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
230 #else
231 #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
232 #end if
233 #end for
234 #set $mlabels = ' '.join($mlabels)
235 #set $matrices = ' '.join($matrices)
236 </token>
237
238 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
239 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
240 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
241
242 <xml name="region">
243 <param name="region" type="text" label="Region of the genome to limit the operation"
244 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
245 </xml>
246
247
248
249 <xml name="kmeans_clustering">
250 <conditional name="used_multiple_regions">
251 <param name="used_multiple_regions_options" type="select"
252 label="Did you compute the matrix with more than one groups of regions?"
253 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.">
254 <option value="yes">Yes, I used multiple groups of regions</option>
255 <option value="no">No, I used only one group</option>
256 </param>
257 <when value="no">
258 <conditional name="clustering">
259 <param name="clustering_options" type="select" label="Clustering algorithm">
260 <option value="none">No clustering</option>
261 <option value="kmeans">Kmeans clustering</option>
262 </param>
263 <when value="kmeans">
264 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
265 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
266 </when>
267 <when value="none" />
268 </conditional>
269 </when>
270 <when value="yes" />
271 </conditional>
272 </xml>
273
274 <token name="@KMEANS_CLUSTERING@">
275 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
276 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
277 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
278 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
279 #end if
280 #end if
281 #end if
282 </token>
283
284 <xml name="samFlag">
285 <param name="samFlag" type="integer" optional="true" value=""
286 label="Filter reads based on the SAM flag"
287 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
288 </xml>
289 <xml name="plotNumbers">
290 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
291 label="Plot the correlation value"
292 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
293 </xml>
294 <xml name="doNotExtendPairedEnds">
295 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
296 label="Do not extend paired ends"
297 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
298 </xml>
299
300 <xml name="ignoreDuplicates">
301 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
302 label="Ignore duplicates"
303 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
304 </xml>
305
306 <xml name="minMappingQuality">
307 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
308 label="Minimum mapping quality"
309 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
310 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
311 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
312 </xml>
313
314 <xml name="skipZeros">
315 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
316 label ="Skip zeros"
317 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
318 </xml>
319
320 <xml name="fragmentLength">
321 <param name="fragmentLength" type="integer" value="300" min="1"
322 label="Fragment length used for the sequencing"
323 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
324 </xml>
325
326 <xml name="scaleFactor">
327 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
328 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
329 </xml>
330
331 <xml name="xMax">
332 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
333 label="Max value for the x-axis in counts per bin" />
334 </xml>
335
336 <xml name="filterThreshold">
337 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
338 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
339
340 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
341 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
342 </xml>
343
344
345 <xml name="pseudocount">
346 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
347 </xml>
348 <xml name='matrix_h5_cooler_macro'>
349 <param name='matrix_h5_cooler' type="data" format="h5,cool"
350 label="Matrix to compute on"/>
351 </xml>
352 <xml name='matrix_h5_cooler_multiple_macro'>
353 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
354 label="Matricies to compute on" multiple="true"/>
355 </xml>
356
357
358
359 <xml name='convertFormat_single_macro'>
360 <conditional name="inputFormat_conditional">
361 <param name="inputFormat_selector" type="select" label="Choose input file type">
362 <option value="optionCool" selected="True">cool</option>
363 <option value="optionH5">h5</option>
364 <!-- <option value="optionHic">hic</option> -->
365 <option value="optionHomer">Homer</option>
366 <option value="optionHicpro">HiCPro</option>
367 </param>
368 <when value="optionCool">
369 <expand macro='matrix_h5_cooler_macro' />
370 <param name='correctionName' type='text' label='Correction factors column name'/>
371 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
372 <param name='chromosome' type='text' label='Load only one chromosome'/>
373 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
374
375 </when>
376 <when value="optionH5">
377 <expand macro='matrix_h5_cooler_macro' />
378 </when>
379 <!-- <when value="optionHic">
380 <param name='matrixHic' type='data' format='binary' label='.hic matrix'/>
381 <param name='resolutions' type='text' label='List of resolutions'/>
382 </when> -->
383
384 <when value="optionHomer">
385 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix'/>
386 </when>
387
388 <when value="optionHicpro">
389 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix'/>
390 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file'/>
391 </when>
392 </conditional>
393 </xml>
394
395 <xml name='convertFormat_multiple_macro'>
396 <conditional name="inputFormat_conditional">
397 <param name="inputFormat_selector" type="select" label="Choose input file type">
398 <option value="optionCool" selected="True">cool</option>
399 <option value="optionH5">h5</option>
400 <option value="optionHomer">Homer</option>
401 <option value="optionHicpro">HiCPro</option>
402 </param>
403 <when value="optionCool">
404 <expand macro='matrix_h5_cooler_multiple_macro' />
405 <param name='correctionName' type='text' label='Correction factors column name'/>
406 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
407 <param name='chromosome' type='text' label='Load only one chromosome'/>
408 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
409
410 </when>
411 <when value="optionH5">
412 <expand macro='matrix_h5_cooler_multiple_macro' />
413 </when>
414
415 <when value="optionHomer">
416 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' multiple="true"/>
417 </when>
418
419 <when value="optionHicpro">
420 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/>
421 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/>
422 </when>
423 </conditional>
424 </xml>
425 <xml name='convertFormat_single_output_macro'>
426 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
427
428 <conditional name="outputFormat_conditional">
429 <param name="outputFormat_selector" type="select" label="Choose output file type">
430 <option value="cool" selected="True">cool</option>
431 <option value="h5">h5</option>
432 <option value="homer">Homer</option>
433 <option value="ginteractions">ginteractions</option>
434
435 </param>
436 <when value="cool">
437 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count'/>
438 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column'/>
439 </when>
440 <when value='h5'/>
441 <when value='homer'/>
442 <when value='ginteractions'/>
443
444 </conditional>
445 </xml>
446 <token name="@REFERENCES@">
447
448 .. class:: infomark
449
450 For more information on the tools, please visit our `help site`_.
451
452 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
453
454 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
455
456 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
457 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
458 .. _help site: https://hicexplorer.readthedocs.org
459
460 </token>
461
462
463 <xml name="multiple_input_bams">
464 <repeat name="input_files" title="BAM files" min="2">
465 <param name="bamfile" type="data" format="bam"
466 label="Bam file"
467 help="The BAM file must be sorted."/>
468 <param name="label" type="text" size="30" optional="true" value=""
469 label="Label"
470 help="Label to use in the output. If not given the dataset name will be used instead."/>
471 </repeat>
472 </xml>
473
474 <xml name="multiple_input_bigwigs">
475 <repeat name="input_files" title="BigWig files" min="2">
476 <param name="bigwigfile" type="data" format="bigwig"
477 label="Bigwig file"
478 help="The Bigwig file must be sorted."/>
479 <param name="label" type="text" size="30" optional="true" value=""
480 label="Label"
481 help="Label to use in the output. If not given the dataset name will be used instead."/>
482 </repeat>
483 </xml>
484
485 <xml name="plotTitle">
486 <param name="plotTitle" type="text" value="" size="30" optional="True"
487 label="Title of the plot"
488 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
489 </xml>
490
491 <token name="@multiple_input_bams@">
492 #import tempfile
493 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
494 #set files=[]
495 #set labels=[]
496 #for $i in $input_files:
497 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
498 #set $temp_input_path = $temp_input_handle.name
499 #silent $temp_input_handle.close()
500 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
501 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
502 #silent $files.append('%s.bam' % $temp_input_path)
503
504 ##set $files += [str($i.bamfile)]
505 #if str($i.label.value) != "":
506 #set $labels += ["\"%s\"" % ($i.label.value)]
507 #else
508 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
509 #end if
510 #end for
511 </token>
512
513 <token name="@multiple_input_bigwigs@">
514 #import tempfile
515 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
516 #set files=[]
517 #set labels=[]
518 #for $i in $input_files:
519 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
520 #set $temp_input_path = $temp_input_handle.name
521 #silent $temp_input_handle.close()
522 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
523 #silent $files.append('%s.bw' % $temp_input_path)
524
525 ##set $files += [str($i.bigwigfile)]
526 #if str($i.label.value) != "":
527 #set $labels += ["\"%s\"" % ($i.label.value)]
528 #else
529 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
530 #end if
531 #end for
532 </token>
533
534 <xml name="reference_genome_source">
535 <conditional name="source">
536 <param name="ref_source" type="select" label="Reference genome">
537 <option value="cached">locally cached</option>
538 <option value="history">in your history</option>
539 </param>
540 <when value="cached">
541 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
542 <options from_data_table="deepTools_seqs">
543 <filter type="sort_by" column="1" />
544 <validator type="no_options" message="No indexes are available." />
545 </options>
546 </param>
547 </when>
548 <when value="history">
549 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
550 </when>
551 </conditional>
552 </xml>
553
554 <token name="@reference_genome_source@">
555 #if $source.ref_source=="history":
556 --genome $source.input1
557 #else:
558 --genome "${source.input1_2bit.fields.path}"
559 #end if
560 </token>
561
562 <xml name="effectiveGenomeSize">
563 <conditional name="effectiveGenomeSize">
564 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
565 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.
566 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
567 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.">
568 <option value="93260000">ce10 (93260000)</option>
569 <option value="121400000">dm3 (121400000)</option>
570 <option value="2451960000" selected="true">hg19 (2451960000)</option>
571 <option value="2150570000">mm9 (2150570000)</option>
572 <option value="specific">user specified</option>
573 </param>
574 <when value="specific">
575 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
576 </when>
577 <when value="2150570000" />
578 <when value="2451960000" />
579 <when value="121400000" />
580 <when value="93260000" />
581 </conditional>
582 </xml>
583
584 <xml name="image_file_format">
585 <param name="outFileFormat" type="select" label="Image file format">
586 <option value="png" selected="true">png</option>
587 <option value="pdf">pdf</option>
588 <option value="svg">svg</option>
589 <option value="eps">eps</option>
590 <option value="emf">emf</option>
591 </param>
592 </xml>
593
594 <xml name="missingDataAsZero">
595 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
596 label ="Treat missing data as zero"
597 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
598 </xml>
599
600 <xml name="input_save_matrix_values">
601 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
602 </xml>
603
604 <xml name="input_graphic_output_settings">
605 <conditional name="output" >
606 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
607 <option value="no" selected="true">no</option>
608 <option value="yes">yes</option>
609 </param>
610 <when value="no" />
611 <when value="yes">
612 <yield />
613 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
614 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
615 </when>
616 </conditional>
617 </xml>
618
619 <xml name="input_image_file_format">
620 <param name="outFileFormat" type="select" label="Image file format">
621 <option value="png" selected="true">png</option>
622 <option value="pdf">pdf</option>
623 <option value="svg">svg</option>
624 <option value="eps">eps</option>
625 <option value="emf">emf</option>
626 </param>
627 </xml>
628
629 <xml name="output_image_file_format">
630 <data format="png" name="outFileName" label="${tool.name} image">
631 <change_format>
632 <when input="output.outFileFormat" value="pdf" format="pdf" />
633 <when input="output.outFileFormat" value="svg" format="svg" />
634 <when input="output.outFileFormat" value="eps" format="eps" />
635 <when input="output.outFileFormat" value="emf" format="emf" />
636 </change_format>
637 </data>
638 </xml>
639
640 <xml name="output_save_matrix_values">
641 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
642 <filter>
643 ((
644 output['showOutputSettings'] == 'yes' and
645 output['saveMatrix'] is True
646 ))
647 </filter>
648 </data>
649 </xml>
650
651 <xml name="output_graphic_outputs">
652 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
653 <filter>
654 ((
655 output['showOutputSettings'] == 'yes' and
656 output['saveData'] is True
657 ))
658 </filter>
659 </data>
660 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
661 <filter>
662 ((
663 output['showOutputSettings'] == 'yes' and
664 output['saveSortedRegions'] is True
665 ))
666 </filter>
667 </data>
668 </xml>
669
670 <xml name="track_input_h5_macro">
671 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
672 </xml>
673 <xml name="track_input_bed_macro">
674 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
675 </xml>
676 <xml name="track_input_bedgraph_macro">
677 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
678 </xml>
679 <xml name="track_input_bigwig_macro">
680 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
681 </xml>
682 <xml name="track_input_bedgraph_matrix_macro">
683 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
684 </xml>
685 <xml name="track_input_tabular_macro">
686 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
687 </xml>
688 <xml name="plot_title">
689 <param name="title" type="text" optional="true" label="Plot title"/>
690 </xml>
691
692 <xml name="spacer_macro">
693 <param name="spacer_width" type="float" value="" optional="True"
694 label="Include spacer at the end of the track." help="Width of the spacer." />
695 </xml>
696 <xml name="fontsize_macro">
697 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
698 </xml>
699 </macros>