Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison macros.xml @ 25:8f0ad6a9476f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 19:11:51 +0000
parents 4fa8acf5581c
children 98c63c21b144
comparison
equal deleted inserted replaced
24:4fa8acf5581c 25:8f0ad6a9476f
1 <macros> 1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> 2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <token name="@TOOL_VERSION@">3.6</token> 3 <token name="@TOOL_VERSION@">3.7.5</token>
4 <token name="@VERSION_SUFFIX@">1</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">23.0</token>
5 <token name="@USE_RANGE@"> 6 <token name="@USE_RANGE@">
6 #if $use_range.select_use_range == "yes_use_range": 7 #if $use_range.select_use_range == "yes_use_range":
7 --range $use_range.range_min:$use_range.range_max 8 --range $use_range.range_min:$use_range.range_max
8 #end if 9 #end if
9 </token> 10 </token>
35 </repeat> 36 </repeat>
36 </xml> 37 </xml>
37 38
38 <xml name="citations"> 39 <xml name="citations">
39 <citations> 40 <citations>
40 <citation type="doi">10.5281/zenodo.1133705</citation> 41 <citation type="doi">10.1093/nar/gkaa220</citation>
42 <citation type="doi">10.1093/nar/gky504</citation>
41 <yield /> 43 <yield />
42 </citations> 44 </citations>
43 </xml> 45 </xml>
44 <xml name="dpi"> 46 <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.' /> 47 <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
245 247
246 <token name="@multiple_input_matrices@"> 248 <token name="@multiple_input_matrices@">
247 #set $matrices = [] 249 #set $matrices = []
248 #set $mlabels = [] 250 #set $mlabels = []
249 #for $counter, $i in enumerate($input_files): 251 #for $counter, $i in enumerate($input_files):
250 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; 252 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
251 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext)) 253 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
252 254
253 #if str($i.mlabel.value) != "": 255 #if str($i.mlabel.value) != "":
254 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)] 256 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
255 #else 257 #else
346 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" /> 348 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" />
347 </xml> 349 </xml>
348 <xml name='matrix_h5_cooler_multiple_macro'> 350 <xml name='matrix_h5_cooler_multiple_macro'>
349 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" /> 351 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" />
350 </xml> 352 </xml>
353
354 <xml name='matrix_cooler_multiple_macro'>
355 <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" />
356 </xml>
351 <xml name='convertFormat_single_macro'> 357 <xml name='convertFormat_single_macro'>
352 <conditional name="inputFormat_conditional"> 358 <conditional name="inputFormat_conditional">
353 <param name="inputFormat_selector" type="select" label="Choose input file type"> 359 <param name="inputFormat_selector" type="select" label="Choose input file type">
354 <option value="optionCool" selected="True">cool</option> 360 <option value="optionCool" selected="True">cool</option>
355 <option value="optionH5">h5</option> 361 <option value="optionH5">h5</option>
356 <option value="optionHic">hic</option> 362 <option value="optionHic">hic</option>
357 <option value="optionHomer">Homer</option> 363 <option value="optionHomer">Homer</option>
358 <option value="optionHicpro">HiCPro</option> 364 <option value="optionHicpro">HiCPro</option>
365 <option value="option2Dtext">2D-text</option>
366
359 </param> 367 </param>
360 <when value="optionCool"> 368 <when value="optionCool">
361 <expand macro='matrix_h5_cooler_macro' /> 369 <expand macro='matrix_h5_cooler_macro' />
362 <param name='correctionName' type='text' label='Correction factors column name' /> 370 <param name='correctionName' type='text' label='Correction factors column name' />
363 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' /> 371 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
375 </when> 383 </when>
376 <when value="optionHomer"> 384 <when value="optionHomer">
377 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' /> 385 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
378 </when> 386 </when>
379 <when value="optionHicpro"> 387 <when value="optionHicpro">
380 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' /> 388 <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' />
381 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' /> 389 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
390 </when>
391 <when value="option2Dtext">
392 <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' />
393
394 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
395 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
396 </param>
397 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
382 </when> 398 </when>
383 </conditional> 399 </conditional>
384 </xml> 400 </xml>
385 401
386 <xml name='convertFormat_multiple_macro'> 402 <xml name='convertFormat_multiple_macro'>
388 <param name="inputFormat_selector" type="select" label="Choose input file type"> 404 <param name="inputFormat_selector" type="select" label="Choose input file type">
389 <option value="optionCool" selected="True">cool</option> 405 <option value="optionCool" selected="True">cool</option>
390 <option value="optionH5">h5</option> 406 <option value="optionH5">h5</option>
391 <option value="optionHomer">Homer</option> 407 <option value="optionHomer">Homer</option>
392 <option value="optionHicpro">HiCPro</option> 408 <option value="optionHicpro">HiCPro</option>
409 <option value="option2Dtext">2D-text</option>
410
411
393 </param> 412 </param>
394 <when value="optionCool"> 413 <when value="optionCool">
395 <expand macro='matrix_h5_cooler_multiple_macro' /> 414 <expand macro='matrix_h5_cooler_multiple_macro' />
396 <param name='correctionName' type='text' label='Correction factors column name' /> 415 <param name='correctionName' type='text' label='Correction factors column name' />
397 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' /> 416 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
405 <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' /> 424 <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' />
406 </when> 425 </when>
407 <when value="optionHicpro"> 426 <when value="optionHicpro">
408 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' /> 427 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
409 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' /> 428 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
429 </when>
430 <when value="option2Dtext">
431 <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' />
432
433 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
434 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
435 </param>
436 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
410 </when> 437 </when>
411 </conditional> 438 </conditional>
412 </xml> 439 </xml>
413 <xml name='convertFormat_single_output_macro'> 440 <xml name='convertFormat_single_output_macro'>
414 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> --> 441 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
416 <param name="outputFormat_selector" type="select" label="Choose output file type"> 443 <param name="outputFormat_selector" type="select" label="Choose output file type">
417 <option value="cool" selected="True">cool</option> 444 <option value="cool" selected="True">cool</option>
418 <option value="h5">h5</option> 445 <option value="h5">h5</option>
419 <option value="homer">Homer</option> 446 <option value="homer">Homer</option>
420 <option value="ginteractions">ginteractions</option> 447 <option value="ginteractions">ginteractions</option>
448 <option value="hicpro">hicpro</option>
449
421 </param> 450 </param>
422 <when value="cool"> 451 <when value="cool">
423 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' /> 452 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
424 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' /> 453 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
425 </when> 454 </when>
426 <when value='h5' /> 455 <when value='h5' />
427 <when value='homer' /> 456 <when value='homer' />
428 <when value='ginteractions' /> 457 <when value='ginteractions' />
458 <when value='hicpro' />
429 </conditional> 459 </conditional>
430 </xml> 460 </xml>
431 <token name="@REFERENCES@"> 461 <token name="@REFERENCES@">
432 462
433 .. class:: infomark 463 .. class:: infomark