Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison macros.xml @ 13:4b85ea34afae 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 15:44:31 -0500
parents 4ceaee0043a5
children 76b189fd277b
comparison
equal deleted inserted replaced
12:8bf84c4cb1cb 13:4b85ea34afae
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@">2.1.4</token> 3 <token name="@WRAPPER_VERSION@">3.3.1</token>
4 <token name="@USE_RANGE@"> 4 <token name="@USE_RANGE@">
5 #if $use_range.select_use_range == "yes_use_range": 5 #if $use_range.select_use_range == "yes_use_range":
6 --range $range_min:$range_max 6 --range $range_min:$range_max
7 #end if 7 #end if
8 </token> 8 </token>
11 <requirements> 11 <requirements>
12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> 12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
13 <yield /> 13 <yield />
14 </requirements> 14 </requirements>
15 <version_command>@BINARY@ --version</version_command> 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>
16 </xml> 35 </xml>
17 36
18 <xml name="citations"> 37 <xml name="citations">
19 <citations> 38 <citations>
20 <citation type="doi">10.5281/zenodo.1133705</citation> 39 <citation type="doi">10.5281/zenodo.1133705</citation>
112 <option value="bwr">bwr</option> 131 <option value="bwr">bwr</option>
113 <option value="hsv">hsv</option> 132 <option value="hsv">hsv</option>
114 <option value="brg">brg</option> 133 <option value="brg">brg</option>
115 <option value="jet">jet</option> 134 <option value="jet">jet</option>
116 <option value="afmhot">afmhot</option> 135 <option value="afmhot">afmhot</option>
136 <option value="plasma">plasma</option>
117 <option value="Accent_r">Accent reversed</option> 137 <option value="Accent_r">Accent reversed</option>
118 <option value="Spectral_r">Spectral reversed</option> 138 <option value="Spectral_r">Spectral reversed</option>
119 <option value="Set1_r">Set1 reversed</option> 139 <option value="Set1_r">Set1 reversed</option>
120 <option value="Set2_r">Set2 reversed</option> 140 <option value="Set2_r">Set2 reversed</option>
121 <option value="Set3_r">Set3 reversed</option> 141 <option value="Set3_r">Set3 reversed</option>
181 <option value="bwr_r">bwr reversed</option> 201 <option value="bwr_r">bwr reversed</option>
182 <option value="hsv_r">hsv reversed</option> 202 <option value="hsv_r">hsv reversed</option>
183 <option value="brg_r">brg reversed</option> 203 <option value="brg_r">brg reversed</option>
184 <option value="jet_r">jet reversed</option> 204 <option value="jet_r">jet reversed</option>
185 <option value="afmhot_r">afmhot reversed</option> 205 <option value="afmhot_r">afmhot reversed</option>
206 <option value="plasma_r">plasma reversed</option>
186 </param> 207 </param>
187 </xml> 208 </xml>
188
189 209
190 <xml name="multiple_input_matrices"> 210 <xml name="multiple_input_matrices">
191 <repeat name="input_files" title="Hi-C Matrix files" min="2"> 211 <repeat name="input_files" title="Hi-C Matrix files" min="2">
192 <param name="matrix" type="data" format="h5,cool" 212 <param name="matrix" type="data" format="h5,cool"
193 label="Hi-C Matrix file" 213 label="Hi-C Matrix file"
200 220
201 <token name="@multiple_input_matrices@"> 221 <token name="@multiple_input_matrices@">
202 #set $matrices = [] 222 #set $matrices = []
203 #set $mlabels = [] 223 #set $mlabels = []
204 #for $counter, $i in enumerate($input_files): 224 #for $counter, $i in enumerate($input_files):
205 ln -s $i.matrix #echo str($counter)+'_matrix'#; 225 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
206 #silent $matrices.append( '%s_matrix' % $counter ) 226 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
207 227
208 #if str($i.mlabel.value) != "": 228 #if str($i.mlabel.value) != "":
209 #set $mlabels += ['"%s"' % ($i.mlabel.value)] 229 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
210 #else 230 #else
211 #set $mlabels += ['"%s"' % ($i.matrix.name)] 231 #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
212 #end if 232 #end if
213 #end for 233 #end for
214 #set $mlabels = ' '.join($mlabels) 234 #set $mlabels = ' '.join($mlabels)
215 #set $matrices = ' '.join($matrices) 235 #set $matrices = ' '.join($matrices)
216 </token> 236 </token>
217 237
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>
218 241
219 <xml name="region"> 242 <xml name="region">
220 <param name="region" type="text" label="Region of the genome to limit the operation" 243 <param name="region" type="text" label="Region of the genome to limit the operation"
221 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/> 244 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
222 </xml> 245 </xml>
327 label="Matrix to compute on"/> 350 label="Matrix to compute on"/>
328 </xml> 351 </xml>
329 <xml name='matrix_h5_cooler_multiple_macro'> 352 <xml name='matrix_h5_cooler_multiple_macro'>
330 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" 353 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
331 label="Matricies to compute on" multiple="true"/> 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>
332 </xml> 445 </xml>
333 <token name="@REFERENCES@"> 446 <token name="@REFERENCES@">
334 447
335 .. class:: infomark 448 .. class:: infomark
336 449