Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison macros.xml @ 16:96c472622ebc draft

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"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
author bgruening
date Mon, 16 Dec 2019 13:20:28 +0000
parents 4053214bebac
children 83bda473a3f7
comparison
equal deleted inserted replaced
15:4053214bebac 16:96c472622ebc
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@">3.3.1</token> 3 <token name="@WRAPPER_VERSION@">2.1.4</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>
35 </xml> 16 </xml>
36 17
37 <xml name="citations"> 18 <xml name="citations">
38 <citations> 19 <citations>
39 <citation type="doi">10.5281/zenodo.1133705</citation> 20 <citation type="doi">10.5281/zenodo.1133705</citation>
131 <option value="bwr">bwr</option> 112 <option value="bwr">bwr</option>
132 <option value="hsv">hsv</option> 113 <option value="hsv">hsv</option>
133 <option value="brg">brg</option> 114 <option value="brg">brg</option>
134 <option value="jet">jet</option> 115 <option value="jet">jet</option>
135 <option value="afmhot">afmhot</option> 116 <option value="afmhot">afmhot</option>
136 <option value="plasma">plasma</option>
137 <option value="Accent_r">Accent reversed</option> 117 <option value="Accent_r">Accent reversed</option>
138 <option value="Spectral_r">Spectral reversed</option> 118 <option value="Spectral_r">Spectral reversed</option>
139 <option value="Set1_r">Set1 reversed</option> 119 <option value="Set1_r">Set1 reversed</option>
140 <option value="Set2_r">Set2 reversed</option> 120 <option value="Set2_r">Set2 reversed</option>
141 <option value="Set3_r">Set3 reversed</option> 121 <option value="Set3_r">Set3 reversed</option>
201 <option value="bwr_r">bwr reversed</option> 181 <option value="bwr_r">bwr reversed</option>
202 <option value="hsv_r">hsv reversed</option> 182 <option value="hsv_r">hsv reversed</option>
203 <option value="brg_r">brg reversed</option> 183 <option value="brg_r">brg reversed</option>
204 <option value="jet_r">jet reversed</option> 184 <option value="jet_r">jet reversed</option>
205 <option value="afmhot_r">afmhot reversed</option> 185 <option value="afmhot_r">afmhot reversed</option>
206 <option value="plasma_r">plasma reversed</option>
207 </param> 186 </param>
208 </xml> 187 </xml>
188
209 189
210 <xml name="multiple_input_matrices"> 190 <xml name="multiple_input_matrices">
211 <repeat name="input_files" title="Hi-C Matrix files" min="2"> 191 <repeat name="input_files" title="Hi-C Matrix files" min="2">
212 <param name="matrix" type="data" format="h5,cool" 192 <param name="matrix" type="data" format="h5,cool"
213 label="Hi-C Matrix file" 193 label="Hi-C Matrix file"
220 200
221 <token name="@multiple_input_matrices@"> 201 <token name="@multiple_input_matrices@">
222 #set $matrices = [] 202 #set $matrices = []
223 #set $mlabels = [] 203 #set $mlabels = []
224 #for $counter, $i in enumerate($input_files): 204 #for $counter, $i in enumerate($input_files):
225 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; 205 ln -s $i.matrix #echo str($counter)+'_matrix'#;
226 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext)) 206 #silent $matrices.append( '%s_matrix' % $counter )
227 207
228 #if str($i.mlabel.value) != "": 208 #if str($i.mlabel.value) != "":
229 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)] 209 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
230 #else 210 #else
231 #set $mlabels += ['\'%s\'' % ($i.matrix.name)] 211 #set $mlabels += ['"%s"' % ($i.matrix.name)]
232 #end if 212 #end if
233 #end for 213 #end for
234 #set $mlabels = ' '.join($mlabels) 214 #set $mlabels = ' '.join($mlabels)
235 #set $matrices = ' '.join($matrices) 215 #set $matrices = ' '.join($matrices)
236 </token> 216 </token>
237 217
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>
241 218
242 <xml name="region"> 219 <xml name="region">
243 <param name="region" type="text" label="Region of the genome to limit the operation" 220 <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"/> 221 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
245 </xml> 222 </xml>
351 </xml> 328 </xml>
352 <xml name='matrix_h5_cooler_multiple_macro'> 329 <xml name='matrix_h5_cooler_multiple_macro'>
353 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" 330 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
354 label="Matricies to compute on" multiple="true"/> 331 label="Matricies to compute on" multiple="true"/>
355 </xml> 332 </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@"> 333 <token name="@REFERENCES@">
447 334
448 .. class:: infomark 335 .. class:: infomark
449 336
450 For more information on the tools, please visit our `help site`_. 337 For more information on the tools, please visit our `help site`_.