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comparison macros.xml @ 11:ee370ade24cd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:21:53 +0000
parents 8286e361f89c
children e30485c5e93b
comparison
equal deleted inserted replaced
10:8286e361f89c 11:ee370ade24cd
1 <macros> 1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> 2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <token name="@WRAPPER_VERSION@">3.4.3</token> 3 <token name="@TOOL_VERSION@">3.6</token>
4 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@USE_RANGE@"> 5 <token name="@USE_RANGE@">
5 #if $use_range.select_use_range == "yes_use_range": 6 #if $use_range.select_use_range == "yes_use_range":
6 --range $use_range.range_min:$use_range.range_max 7 --range $use_range.range_min:$use_range.range_max
7 #end if 8 #end if
8 </token> 9 </token>
9 10
10 <xml name="requirements"> 11 <xml name="requirements">
11 <requirements> 12 <requirements>
12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">hicexplorer</requirement>
13 <yield /> 14 <yield />
14 </requirements> 15 </requirements>
15 <version_command>@BINARY@ --version</version_command> 16 <version_command>@BINARY@ --version</version_command>
16 </xml> 17 </xml>
17 18
26 #end if 27 #end if
27 </token> 28 </token>
28 29
29 <xml name="chromosome_list"> 30 <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 <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 <param argument="--chromosomes" type="text" value="">
32 <validator type="empty_field" /> 33 <validator type="empty_field" />
33 </param> 34 </param>
34 </repeat> 35 </repeat>
35 </xml> 36 </xml>
36 37
38 <citations> 39 <citations>
39 <citation type="doi">10.5281/zenodo.1133705</citation> 40 <citation type="doi">10.5281/zenodo.1133705</citation>
40 <yield /> 41 <yield />
41 </citations> 42 </citations>
42 </xml> 43 </xml>
44 <xml name="dpi">
45 <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
46 </xml>
47
48 <xml name="restrictionCutFile">
49 <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
50 (i.e. the region between one restriction site and the next)." />
51 </xml>
52
53 <xml name="restrictionSequence">
54 <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
55 &quot;dangling-ends&quot;. If not given, such statistics will not be available.">
56 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
57 </param>
58 </xml>
59 <xml name="danglingSequence">
60 <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.
61 Each restriction enzyme recognizes a different DNA sequence and,
62 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
63 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
64 For DpnII, the restriction site and dangling end sequence are the same: GATC.
65 This information is easily found on the description of the restriction enzyme.
66 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
67 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">
68 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
69 </param>
70 </xml>
43 71
44 <xml name="zMax"> 72 <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 --> 73 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />
74 <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
46 </xml> 75 </xml>
47 <xml name="use_range"> 76 <xml name="use_range">
48 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> 77 <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."> 78 <param name="select_use_range" argument="--range" type="select" label="Range restriction (in bp)" help="If given, only counts within the specified range are considered.">
50 <option value="no_use_range">No restriction</option> 79 <option value="no_use_range">No restriction</option>
51 <option value="yes_use_range">Only consider counts within a range</option> 80 <option value="yes_use_range">Only consider counts within a range</option>
52 </param> 81 </param>
53 <when value="no_use_range"/> 82 <when value="no_use_range" />
54 <when value="yes_use_range"> 83 <when value="yes_use_range">
55 <expand macro='range' /> 84 <expand macro='range' />
56 </when> 85 </when>
57 </conditional> 86 </conditional>
58 </xml> 87 </xml>
59 88
60 <xml name="range"> 89 <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."/> 90 <param name='range_min' type="integer" value="" min="0" label="Minimum range to consider interactions" 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"/> 91 <param name='range_max' type="integer" value="" min="0" label="Maximum range to consider interactions" />
63 </xml> 92 </xml>
64 93
65 <xml name="colormap"> 94 <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"> 95 <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> 96 <option value="RdYlBu">RdYlBu</option>
207 </param> 236 </param>
208 </xml> 237 </xml>
209 238
210 <xml name="multiple_input_matrices"> 239 <xml name="multiple_input_matrices">
211 <repeat name="input_files" title="Hi-C Matrix files" min="2"> 240 <repeat name="input_files" title="Hi-C Matrix files" min="2">
212 <param name="matrix" type="data" format="h5,cool" 241 <param name="matrix" type="data" format="h5,cool" label="Hi-C Matrix file" help="" />
213 label="Hi-C Matrix file" 242 <param name="mlabel" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." />
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> 243 </repeat>
219 </xml> 244 </xml>
220 245
221 <token name="@multiple_input_matrices@"> 246 <token name="@multiple_input_matrices@">
222 #set $matrices = [] 247 #set $matrices = []
238 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token> 263 <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> 264 <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> 265 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
241 266
242 <xml name="region"> 267 <xml name="region">
243 <param name="region" type="text" label="Region of the genome to limit the operation" 268 <param argument="--region" type="text" label="Region of the genome to limit the operation" help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500">
244 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/> 269 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator>
245 </xml> 270 </param>
246 271 </xml>
247
248 272
249 <xml name="kmeans_clustering"> 273 <xml name="kmeans_clustering">
250 <conditional name="used_multiple_regions"> 274 <conditional name="used_multiple_regions">
251 <param name="used_multiple_regions_options" type="select" 275 <param name="used_multiple_regions_options" type="select" label="Did you compute the matrix with more than one groups of regions?" 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.">
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> 276 <option value="yes">Yes, I used multiple groups of regions</option>
255 <option value="no">No, I used only one group</option> 277 <option value="no">No, I used only one group</option>
256 </param> 278 </param>
257 <when value="no"> 279 <when value="no">
258 <conditional name="clustering"> 280 <conditional name="clustering">
259 <param name="clustering_options" type="select" label="Clustering algorithm"> 281 <param name="clustering_options" type="select" label="Clustering algorithm">
260 <option value="none">No clustering</option> 282 <option value="none">No clustering</option>
261 <option value="kmeans">Kmeans clustering</option> 283 <option value="kmeans">Kmeans clustering</option>
262 </param> 284 </param>
263 <when value="kmeans"> 285 <when value="kmeans">
264 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" 286 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" 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)." />
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> 287 </when>
267 <when value="none" /> 288 <when value="none" />
268 </conditional> 289 </conditional>
269 </when> 290 </when>
270 <when value="yes" /> 291 <when value="yes" />
280 #end if 301 #end if
281 #end if 302 #end if
282 </token> 303 </token>
283 304
284 <xml name="samFlag"> 305 <xml name="samFlag">
285 <param name="samFlag" type="integer" optional="true" value="" 306 <param name="samFlag" type="integer" optional="true" value="" label="Filter reads based on the SAM flag" 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)" />
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> 307 </xml>
289 <xml name="plotNumbers"> 308 <xml name="plotNumbers">
290 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" 309 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" label="Plot the correlation value" help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)" />
291 label="Plot the correlation value"
292 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
293 </xml> 310 </xml>
294 <xml name="doNotExtendPairedEnds"> 311 <xml name="doNotExtendPairedEnds">
295 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" 312 <param argument="--doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" label="Do not extend paired ends" 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)" />
296 label="Do not extend paired ends" 313 </xml>
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"> 314 <xml name="ignoreDuplicates">
301 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" 315 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" label="Ignore duplicates" 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)" />
302 label="Ignore duplicates" 316 </xml>
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"> 317 <xml name="minMappingQuality">
307 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1" 318 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1" label="Minimum mapping quality" help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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. 319 *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."/> 320 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> 321 </xml>
313 322
314 <xml name="skipZeros"> 323 <xml name="skipZeros">
315 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" 324 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" label="Skip zeros" 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)" />
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> 325 </xml>
319 326
320 <xml name="fragmentLength"> 327 <xml name="fragmentLength">
321 <param name="fragmentLength" type="integer" value="300" min="1" 328 <param argument="--fragmentLength" type="integer" value="300" min="1" label="Fragment length used for the sequencing" help="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)" />
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> 329 </xml>
325 330
326 <xml name="scaleFactor"> 331 <xml name="scaleFactor">
327 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> 332 <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)"/> 333 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" />
329 </xml> 334 </xml>
330
331 <xml name="xMax"> 335 <xml name="xMax">
332 <param argument="--xMax" name="xMax" type="integer" optional="true" value="" 336 <param argument="--xMax" name="xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
333 label="Max value for the x-axis in counts per bin" /> 337 </xml>
334 </xml>
335
336 <xml name="filterThreshold"> 338 <xml name="filterThreshold">
337 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" 339 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect." />
338 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/> 340 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0" label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect." />
339 341 </xml>
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"> 342 <xml name="pseudocount">
346 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> 343 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero." />
347 </xml> 344 </xml>
348 <xml name='matrix_h5_cooler_macro'> 345 <xml name='matrix_h5_cooler_macro'>
349 <param name='matrix_h5_cooler' type="data" format="h5,cool" 346 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" />
350 label="Matrix to compute on"/>
351 </xml> 347 </xml>
352 <xml name='matrix_h5_cooler_multiple_macro'> 348 <xml name='matrix_h5_cooler_multiple_macro'>
353 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" 349 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" />
354 label="Matricies to compute on" multiple="true"/> 350 </xml>
355 </xml>
356
357
358
359 <xml name='convertFormat_single_macro'> 351 <xml name='convertFormat_single_macro'>
360 <conditional name="inputFormat_conditional"> 352 <conditional name="inputFormat_conditional">
361 <param name="inputFormat_selector" type="select" label="Choose input file type"> 353 <param name="inputFormat_selector" type="select" label="Choose input file type">
362 <option value="optionCool" selected="True">cool</option> 354 <option value="optionCool" selected="True">cool</option>
363 <option value="optionH5">h5</option> 355 <option value="optionH5">h5</option>
365 <option value="optionHomer">Homer</option> 357 <option value="optionHomer">Homer</option>
366 <option value="optionHicpro">HiCPro</option> 358 <option value="optionHicpro">HiCPro</option>
367 </param> 359 </param>
368 <when value="optionCool"> 360 <when value="optionCool">
369 <expand macro='matrix_h5_cooler_macro' /> 361 <expand macro='matrix_h5_cooler_macro' />
370 <param name='correctionName' type='text' label='Correction factors column name'/> 362 <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'/> 363 <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'/> 364 <param name='chromosome' type='text' label='Load only one chromosome' />
373 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/> 365 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
374
375 </when> 366 </when>
376 <when value="optionH5"> 367 <when value="optionH5">
377 <expand macro='matrix_h5_cooler_macro' /> 368 <expand macro='matrix_h5_cooler_macro' />
378 </when> 369 </when>
379 <when value="optionHic"> 370 <when value="optionHic">
380 <param name='matrixHic' type='data' format='hic' label='.hic matrix'/> 371 <param name='matrixHic' type='data' format='hic' label='.hic matrix' />
381 <param name='resolutions' type='text' label='List of resolutions'/> 372 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
382 </when> 373 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
383 374 </param>
375 </when>
384 <when value="optionHomer"> 376 <when value="optionHomer">
385 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix'/> 377 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
386 </when> 378 </when>
387
388 <when value="optionHicpro"> 379 <when value="optionHicpro">
389 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix'/> 380 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' />
390 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file'/> 381 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
391 </when> 382 </when>
392 </conditional> 383 </conditional>
393 </xml> 384 </xml>
394 385
395 <xml name='convertFormat_multiple_macro'> 386 <xml name='convertFormat_multiple_macro'>
400 <option value="optionHomer">Homer</option> 391 <option value="optionHomer">Homer</option>
401 <option value="optionHicpro">HiCPro</option> 392 <option value="optionHicpro">HiCPro</option>
402 </param> 393 </param>
403 <when value="optionCool"> 394 <when value="optionCool">
404 <expand macro='matrix_h5_cooler_multiple_macro' /> 395 <expand macro='matrix_h5_cooler_multiple_macro' />
405 <param name='correctionName' type='text' label='Correction factors column name'/> 396 <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'/> 397 <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'/> 398 <param name='chromosome' type='text' label='Load only one chromosome' />
408 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/> 399 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
409
410 </when> 400 </when>
411 <when value="optionH5"> 401 <when value="optionH5">
412 <expand macro='matrix_h5_cooler_multiple_macro' /> 402 <expand macro='matrix_h5_cooler_multiple_macro' />
413 </when> 403 </when>
414
415 <when value="optionHomer"> 404 <when value="optionHomer">
416 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' multiple="true"/> 405 <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' />
417 </when> 406 </when>
418
419 <when value="optionHicpro"> 407 <when value="optionHicpro">
420 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/> 408 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
421 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/> 409 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
422 </when> 410 </when>
423 </conditional> 411 </conditional>
424 </xml> 412 </xml>
425 <xml name='convertFormat_single_output_macro'> 413 <xml name='convertFormat_single_output_macro'>
426 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> --> 414 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
427
428 <conditional name="outputFormat_conditional"> 415 <conditional name="outputFormat_conditional">
429 <param name="outputFormat_selector" type="select" label="Choose output file type"> 416 <param name="outputFormat_selector" type="select" label="Choose output file type">
430 <option value="cool" selected="True">cool</option> 417 <option value="cool" selected="True">cool</option>
431 <option value="h5">h5</option> 418 <option value="h5">h5</option>
432 <option value="homer">Homer</option> 419 <option value="homer">Homer</option>
433 <option value="ginteractions">ginteractions</option> 420 <option value="ginteractions">ginteractions</option>
434
435 </param> 421 </param>
436 <when value="cool"> 422 <when value="cool">
437 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count'/> 423 <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'/> 424 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
439 </when> 425 </when>
440 <when value='h5'/> 426 <when value='h5' />
441 <when value='homer'/> 427 <when value='homer' />
442 <when value='ginteractions'/> 428 <when value='ginteractions' />
443
444 </conditional> 429 </conditional>
445 </xml> 430 </xml>
446 <token name="@REFERENCES@"> 431 <token name="@REFERENCES@">
447 432
448 .. class:: infomark 433 .. class:: infomark
457 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de 442 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
458 .. _help site: https://hicexplorer.readthedocs.org 443 .. _help site: https://hicexplorer.readthedocs.org
459 444
460 </token> 445 </token>
461 446
462
463 <xml name="multiple_input_bams"> 447 <xml name="multiple_input_bams">
464 <repeat name="input_files" title="BAM files" min="2"> 448 <repeat name="input_files" title="BAM files" min="2">
465 <param name="bamfile" type="data" format="bam" 449 <param name="bamfile" type="data" format="bam" label="BAM file" />
466 label="Bam file" 450 <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." />
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> 451 </repeat>
472 </xml> 452 </xml>
473 453
474 <xml name="multiple_input_bigwigs"> 454 <xml name="multiple_input_bigwigs">
475 <repeat name="input_files" title="BigWig files" min="2"> 455 <repeat name="input_files" title="BigWig files" min="2">
476 <param name="bigwigfile" type="data" format="bigwig" 456 <param name="bigwigfile" type="data" format="bigwig" label="Bigwig file" />
477 label="Bigwig file" 457 <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead.">
478 help="The Bigwig file must be sorted."/> 458 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
479 <param name="label" type="text" size="30" optional="true" value="" 459 </param>
480 label="Label"
481 help="Label to use in the output. If not given the dataset name will be used instead."/>
482 </repeat> 460 </repeat>
483 </xml> 461 </xml>
484 462
485 <xml name="plotTitle"> 463 <xml name="plotTitle">
486 <param name="plotTitle" type="text" value="" size="30" optional="True" 464 <param name="plotTitle" type="text" value="" optional="True" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. (--plotTitle)">
487 label="Title of the plot" 465 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
488 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" /> 466 </param>
489 </xml> 467 </xml>
490 468
491 <token name="@multiple_input_bams@"> 469 <token name="@multiple_input_bams@">
492 #import tempfile 470 #import tempfile
493 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) 471 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
559 #end if 537 #end if
560 </token> 538 </token>
561 539
562 <xml name="effectiveGenomeSize"> 540 <xml name="effectiveGenomeSize">
563 <conditional name="effectiveGenomeSize"> 541 <conditional name="effectiveGenomeSize">
564 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" 542 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" 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.
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. 543 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."> 544 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> 545 <option value="93260000">ce10 (93260000)</option>
569 <option value="121400000">dm3 (121400000)</option> 546 <option value="121400000">dm3 (121400000)</option>
570 <option value="2451960000" selected="true">hg19 (2451960000)</option> 547 <option value="2451960000" selected="true">hg19 (2451960000)</option>
571 <option value="2150570000">mm9 (2150570000)</option> 548 <option value="2150570000">mm9 (2150570000)</option>
572 <option value="specific">user specified</option> 549 <option value="specific">user specified</option>
573 </param> 550 </param>
574 <when value="specific"> 551 <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"/> 552 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000" />
576 </when> 553 </when>
577 <when value="2150570000" /> 554 <when value="2150570000" />
578 <when value="2451960000" /> 555 <when value="2451960000" />
579 <when value="121400000" /> 556 <when value="121400000" />
580 <when value="93260000" /> 557 <when value="93260000" />
590 <option value="emf">emf</option> 567 <option value="emf">emf</option>
591 </param> 568 </param>
592 </xml> 569 </xml>
593 570
594 <xml name="missingDataAsZero"> 571 <xml name="missingDataAsZero">
595 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" 572 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Treat missing data as zero" 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." />
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> 573 </xml>
599 574
600 <xml name="input_save_matrix_values"> 575 <xml name="input_save_matrix_values">
601 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> 576 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" />
602 </xml> 577 </xml>
603 578
604 <xml name="input_graphic_output_settings"> 579 <xml name="input_graphic_output_settings">
605 <conditional name="output" > 580 <conditional name="output">
606 <param name="showOutputSettings" type="select" label="Show advanced output settings" > 581 <param name="showOutputSettings" type="select" label="Show advanced output settings">
607 <option value="no" selected="true">no</option> 582 <option value="no" selected="true">no</option>
608 <option value="yes">yes</option> 583 <option value="yes">yes</option>
609 </param> 584 </param>
610 <when value="no" /> 585 <when value="no" />
611 <when value="yes"> 586 <when value="yes">
612 <yield /> 587 <yield />
613 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> 588 <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."/> 589 <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> 590 </when>
616 </conditional> 591 </conditional>
617 </xml> 592 </xml>
618 593
619 <xml name="input_image_file_format"> 594 <xml name="input_image_file_format">
666 </filter> 641 </filter>
667 </data> 642 </data>
668 </xml> 643 </xml>
669 644
670 <xml name="track_input_h5_macro"> 645 <xml name="track_input_h5_macro">
671 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/> 646 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format" />
672 </xml> 647 </xml>
673 <xml name="track_input_bed_macro"> 648 <xml name="track_input_bed_macro">
674 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/> 649 <param name="track_input_bed" type="data" format="bed" label="Track file BED format" />
675 </xml> 650 </xml>
676 <xml name="track_input_bedgraph_macro"> 651 <xml name="track_input_bedgraph_macro">
677 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/> 652 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" />
678 </xml> 653 </xml>
679 <xml name="track_input_bigwig_macro"> 654 <xml name="track_input_bigwig_macro">
680 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/> 655 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" />
681 </xml> 656 </xml>
682 <xml name="track_input_bedgraph_matrix_macro"> 657 <xml name="track_input_bedgraph_matrix_macro">
683 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/> 658 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" />
684 </xml> 659 </xml>
685 <xml name="track_input_tabular_macro"> 660 <xml name="track_input_tabular_macro">
686 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/> 661 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format" />
687 </xml> 662 </xml>
688 <xml name="plot_title"> 663 <xml name="plot_title">
689 <param name="title" type="text" optional="true" label="Plot title"/> 664 <param name="title" type="text" optional="true" label="Plot title">
665 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
666 </param>
690 </xml> 667 </xml>
691 668
692 <xml name="spacer_macro"> 669 <xml name="spacer_macro">
693 <param name="spacer_width" type="float" value="" optional="True" 670 <param name="spacer_width" type="float" value="" min="0" optional="True" label="Include spacer at the end of the track" help="Width of the spacer." />
694 label="Include spacer at the end of the track." help="Width of the spacer." />
695 </xml> 671 </xml>
696 <xml name="fontsize_macro"> 672 <xml name="fontsize_macro">
697 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 673 <param name="fontsize" type="integer" value="" min="5" optional="True" label="Fontsize" />
698 </xml> 674 </xml>
699 </macros> 675 </macros>