Mercurial > repos > bgruening > hicexplorer_hicadjustmatrix
comparison macros.xml @ 8:2dccb6bb0add draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 10:42:59 +0000 |
| parents | aeacaf08bd52 |
| children | e06265d204f6 |
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| 7:aeacaf08bd52 | 8:2dccb6bb0add |
|---|---|
| 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 |