Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison macros.xml @ 21:ed2cca6b5de4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:48:01 +0000
parents 29f66c353bcb
children a4c13ddcc8ee
comparison
equal deleted inserted replaced
20:29f66c353bcb 21:ed2cca6b5de4
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@">3.7.2</token>
4 <token name="@VERSION_SUFFIX@">1</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@USE_RANGE@"> 5 <token name="@USE_RANGE@">
6 #if $use_range.select_use_range == "yes_use_range": 6 #if $use_range.select_use_range == "yes_use_range":
7 --range $use_range.range_min:$use_range.range_max 7 --range $use_range.range_min:$use_range.range_max
8 #end if 8 #end if
9 </token> 9 </token>
35 </repeat> 35 </repeat>
36 </xml> 36 </xml>
37 37
38 <xml name="citations"> 38 <xml name="citations">
39 <citations> 39 <citations>
40 <citation type="doi">10.5281/zenodo.1133705</citation> 40 <citation type="doi">10.1093/nar/gkaa220</citation>
41 <citation type="doi">10.1093/nar/gky504</citation>
41 <yield /> 42 <yield />
42 </citations> 43 </citations>
43 </xml> 44 </xml>
44 <xml name="dpi"> 45 <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 <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
346 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" /> 347 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" />
347 </xml> 348 </xml>
348 <xml name='matrix_h5_cooler_multiple_macro'> 349 <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" /> 350 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" />
350 </xml> 351 </xml>
352
353 <xml name='matrix_cooler_multiple_macro'>
354 <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" />
355 </xml>
351 <xml name='convertFormat_single_macro'> 356 <xml name='convertFormat_single_macro'>
352 <conditional name="inputFormat_conditional"> 357 <conditional name="inputFormat_conditional">
353 <param name="inputFormat_selector" type="select" label="Choose input file type"> 358 <param name="inputFormat_selector" type="select" label="Choose input file type">
354 <option value="optionCool" selected="True">cool</option> 359 <option value="optionCool" selected="True">cool</option>
355 <option value="optionH5">h5</option> 360 <option value="optionH5">h5</option>
356 <option value="optionHic">hic</option> 361 <option value="optionHic">hic</option>
357 <option value="optionHomer">Homer</option> 362 <option value="optionHomer">Homer</option>
358 <option value="optionHicpro">HiCPro</option> 363 <option value="optionHicpro">HiCPro</option>
364 <option value="option2Dtext">2D-text</option>
365
359 </param> 366 </param>
360 <when value="optionCool"> 367 <when value="optionCool">
361 <expand macro='matrix_h5_cooler_macro' /> 368 <expand macro='matrix_h5_cooler_macro' />
362 <param name='correctionName' type='text' label='Correction factors column name' /> 369 <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' /> 370 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
375 </when> 382 </when>
376 <when value="optionHomer"> 383 <when value="optionHomer">
377 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' /> 384 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
378 </when> 385 </when>
379 <when value="optionHicpro"> 386 <when value="optionHicpro">
380 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' /> 387 <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' />
381 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' /> 388 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
389 </when>
390 <when value="option2Dtext">
391 <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' />
392
393 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
394 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
395 </param>
396 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
382 </when> 397 </when>
383 </conditional> 398 </conditional>
384 </xml> 399 </xml>
385 400
386 <xml name='convertFormat_multiple_macro'> 401 <xml name='convertFormat_multiple_macro'>
388 <param name="inputFormat_selector" type="select" label="Choose input file type"> 403 <param name="inputFormat_selector" type="select" label="Choose input file type">
389 <option value="optionCool" selected="True">cool</option> 404 <option value="optionCool" selected="True">cool</option>
390 <option value="optionH5">h5</option> 405 <option value="optionH5">h5</option>
391 <option value="optionHomer">Homer</option> 406 <option value="optionHomer">Homer</option>
392 <option value="optionHicpro">HiCPro</option> 407 <option value="optionHicpro">HiCPro</option>
408 <option value="option2Dtext">2D-text</option>
409
410
393 </param> 411 </param>
394 <when value="optionCool"> 412 <when value="optionCool">
395 <expand macro='matrix_h5_cooler_multiple_macro' /> 413 <expand macro='matrix_h5_cooler_multiple_macro' />
396 <param name='correctionName' type='text' label='Correction factors column name' /> 414 <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' /> 415 <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' /> 423 <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' />
406 </when> 424 </when>
407 <when value="optionHicpro"> 425 <when value="optionHicpro">
408 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' /> 426 <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' /> 427 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
428 </when>
429 <when value="option2Dtext">
430 <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' />
431
432 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
433 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
434 </param>
435 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
410 </when> 436 </when>
411 </conditional> 437 </conditional>
412 </xml> 438 </xml>
413 <xml name='convertFormat_single_output_macro'> 439 <xml name='convertFormat_single_output_macro'>
414 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> --> 440 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
416 <param name="outputFormat_selector" type="select" label="Choose output file type"> 442 <param name="outputFormat_selector" type="select" label="Choose output file type">
417 <option value="cool" selected="True">cool</option> 443 <option value="cool" selected="True">cool</option>
418 <option value="h5">h5</option> 444 <option value="h5">h5</option>
419 <option value="homer">Homer</option> 445 <option value="homer">Homer</option>
420 <option value="ginteractions">ginteractions</option> 446 <option value="ginteractions">ginteractions</option>
447 <option value="hicpro">hicpro</option>
448
421 </param> 449 </param>
422 <when value="cool"> 450 <when value="cool">
423 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' /> 451 <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' /> 452 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
425 </when> 453 </when>
426 <when value='h5' /> 454 <when value='h5' />
427 <when value='homer' /> 455 <when value='homer' />
428 <when value='ginteractions' /> 456 <when value='ginteractions' />
457 <when value='hicpro' />
429 </conditional> 458 </conditional>
430 </xml> 459 </xml>
431 <token name="@REFERENCES@"> 460 <token name="@REFERENCES@">
432 461
433 .. class:: infomark 462 .. class:: infomark