Mercurial > repos > jjohnson > encyclopedia_quantify
comparison macros.xml @ 1:acf6acfc8632 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
author | jjohnson |
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date | Wed, 01 Jul 2020 11:24:39 -0400 |
parents | d3a6bc607825 |
children | 174886084dc5 |
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0:d3a6bc607825 | 1:acf6acfc8632 |
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1 <macros> | 1 <macros> |
2 <!-- | |
3 # generate a Walnut CLIB from GPF-DIA and a FASTA | |
4 for i in library/*.mzML; do | |
5 java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -walnut -i $i -f uniprot_yeast_25jan2019.fasta; | |
6 done | |
7 java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -libexport -walnut -o chromatogram_library.elib -i library -f uniprot_yeast_25jan2019.fasta -a false; | |
8 | |
9 # process single-injection DIA with the CLIB | |
10 for i in quant/*.mzML; do | |
11 java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -i $i -l chromatogram_library.elib -f uniprot_yeast_25jan2019.fasta; | |
12 done | |
13 | |
14 Next for Prosit: | |
15 # generate an EncyclopeDIA CLIB from GPF-DIA and a Prosit Library | |
16 for i in library/*.mzML; do | |
17 java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -i $i -l prosit_library.dlib -f uniprot_yeast_25jan2019.fasta; | |
18 done | |
19 java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -libexport -o chromatogram_library.elib -i library -f uniprot_yeast_25jan2019.fasta -a false; | |
20 | |
21 # process single-injection DIA with the CLIB (exactly the same as with Walnut) | |
22 for i in quant/*.mzML; do | |
23 java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -i $i -l chromatogram_library.elib -f uniprot_yeast_25jan2019.fasta; | |
24 done | |
25 --> | |
26 <token name="@VERSION@">0.9.5</token> | 2 <token name="@VERSION@">0.9.5</token> |
27 <xml name="requirements"> | 3 <xml name="requirements"> |
28 <requirements> | 4 <requirements> |
29 <requirement type="package" version="@VERSION@">encyclopedia</requirement> | 5 <requirement type="package" version="@VERSION@">encyclopedia</requirement> |
30 <yield/> | 6 <yield/> |
31 </requirements> | 7 </requirements> |
32 </xml> | 8 </xml> |
9 | |
33 <token name="@ENCYCLOPEDIA_WIKI@"> | 10 <token name="@ENCYCLOPEDIA_WIKI@"> |
34 EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. | 11 EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. |
35 | 12 |
36 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home | 13 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home |
37 </token> | 14 </token> |
41 <citation type="doi">10.1038/s41467-020-15346-1</citation> | 18 <citation type="doi">10.1038/s41467-020-15346-1</citation> |
42 <citation type="doi">10.1074/mcp.P119.001913</citation> | 19 <citation type="doi">10.1074/mcp.P119.001913</citation> |
43 <yield/> | 20 <yield/> |
44 </citations> | 21 </citations> |
45 </xml> | 22 </xml> |
23 | |
46 <token name="@CMD_IMPORTS@"> | 24 <token name="@CMD_IMPORTS@"> |
47 #import re | 25 #import re |
48 #def identifier_or_name($input1) | 26 #def identifier_or_name($input1) |
49 #if hasattr($input1, 'element_identifier') | 27 #if hasattr($input1, 'element_identifier') |
50 #return $input1.element_identifier | 28 #return $input1.element_identifier |
205 <xml name="walnut_common_options"> | 183 <xml name="walnut_common_options"> |
206 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true" | 184 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true" |
207 token_cid_selected="false" token_hcd_selected="true"/> | 185 token_cid_selected="false" token_hcd_selected="true"/> |
208 </xml> | 186 </xml> |
209 <token name="@COMMON_OPTIONS@"> | 187 <token name="@COMMON_OPTIONS@"> |
210 #if $acquisition.set_acquisition == 'yes' | 188 #if $options.acquisition.set_acquisition == 'yes' |
211 -numberOfExtraDecoyLibrariesSearched $acquisition.numberOfExtraDecoyLibrariesSearched | 189 -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched |
212 #if $acquisition.acquisition | 190 #if $options.acquisition.acquisition |
213 -acquisition '$acquisition.acquisition' | 191 -acquisition '$options.acquisition.acquisition' |
214 #end if | 192 #end if |
215 #if $acquisition.enzyme: | 193 #if $options.acquisition.enzyme: |
216 -enzyme '$acquisition.enzyme' | 194 -enzyme '$options.acquisition.enzyme' |
217 #end if | 195 #end if |
218 #if $acquisition.frag: | 196 #if $options.acquisition.frag: |
219 -frag '$acquisition.frag' | 197 -frag '$options.acquisition.frag' |
220 #end if | 198 #end if |
221 #end if | 199 #end if |
222 </token> | 200 </token> |
223 | 201 |
224 <xml name="mass_tolerance"> | 202 <xml name="mass_tolerance"> |
264 <yield/> | 242 <yield/> |
265 </when> | 243 </when> |
266 </conditional> | 244 </conditional> |
267 </xml> | 245 </xml> |
268 <token name="@MASS_TOLERANCE@"> | 246 <token name="@MASS_TOLERANCE@"> |
269 #if $tolerance.set_tolerance == 'yes' | 247 #if $options.tolerance.set_tolerance == 'yes' |
270 -ptolunits $tolerance.precursor_tolerance.ptolunits | 248 -ptolunits $options.tolerance.precursor_tolerance.ptolunits |
271 -ptol $tolerance.precursor_tolerance.ptol | 249 -ptol $options.tolerance.precursor_tolerance.ptol |
272 -ftolunits $tolerance.fragment_tolerance.ftolunits | 250 -ftolunits $options.tolerance.fragment_tolerance.ftolunits |
273 -ftol $tolerance.fragment_tolerance.ftol | 251 -ftol $options.tolerance.fragment_tolerance.ftol |
274 #end if | 252 #end if |
275 </token> | 253 </token> |
276 | 254 |
277 <xml name="mass_library_tolerance"> | 255 <xml name="mass_library_tolerance"> |
278 <expand macro="mass_tolerance"> | 256 <expand macro="mass_tolerance"> |
296 </conditional> | 274 </conditional> |
297 </expand> | 275 </expand> |
298 </xml> | 276 </xml> |
299 <token name="@MASS_LIBRARY_TOLERANCE@"> | 277 <token name="@MASS_LIBRARY_TOLERANCE@"> |
300 @MASS_TOLERANCE@ | 278 @MASS_TOLERANCE@ |
301 #if $tolerance.set_tolerance == 'yes' and $tolerance.library_tolerance.ltolunits != 'defaults' | 279 #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults' |
302 -ltolunits $tolerance.library_tolerance.ltolunits | 280 -ltolunits $options.tolerance.library_tolerance.ltolunits |
303 -ltol $tolerance.library_tolerance.ltol | 281 -ltol $options.tolerance.library_tolerance.ltol |
304 #end if | 282 #end if |
305 </token> | 283 </token> |
306 | 284 |
307 <xml name="percolator_options"> | 285 <xml name="percolator_options"> |
308 <conditional name="percolator"> | 286 <conditional name="percolator"> |
317 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/> | 295 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/> |
318 </when> | 296 </when> |
319 </conditional> | 297 </conditional> |
320 </xml> | 298 </xml> |
321 <token name="@PERCOLATOR_OPTIONS@"> | 299 <token name="@PERCOLATOR_OPTIONS@"> |
322 #if $percolator.set_percolator == 'yes' | 300 #if $options.percolator.set_percolator == 'yes' |
323 #if str($percolator.percolatorVersionNumber) | 301 #if str($options.percolator.percolatorVersionNumber) |
324 -percolatorVersionNumber $percolator.percolatorVersionNumber | 302 -percolatorVersionNumber $options.percolator.percolatorVersionNumber |
325 #end if | 303 #end if |
326 #if str($percolator.percolatorProteinThreshold) | 304 #if str($options.percolator.percolatorProteinThreshold) |
327 -percolatorProteinThreshold $percolator.percolatorProteinThreshold | 305 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold |
328 #end if | 306 #end if |
329 #if str($percolator.percolatorThreshold) | 307 #if str($options.percolator.percolatorThreshold) |
330 -percolatorThreshold $percolator.percolatorThreshold | 308 -percolatorThreshold $options.percolator.percolatorThreshold |
331 #end if | 309 #end if |
332 #end if | 310 #end if |
333 </token> | 311 </token> |
334 | 312 |
335 <xml name="peak_options"> | 313 <xml name="peak_options"> |
351 </param> | 329 </param> |
352 </when> | 330 </when> |
353 </conditional> | 331 </conditional> |
354 </xml> | 332 </xml> |
355 <token name="@PEAK_OPTIONS@"> | 333 <token name="@PEAK_OPTIONS@"> |
356 #if $peak.set_peak == 'yes' | 334 #if $options.peak.set_peak == 'yes' |
357 #if str($peak.numberOfQuantitativePeaks) | 335 #if str($options.peak.numberOfQuantitativePeaks) |
358 -numberOfQuantitativePeaks $peak.numberOfQuantitativePeaks | 336 -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks |
359 #end if | 337 #end if |
360 #if str($peak.minNumOfQuantitativePeaks) | 338 #if str($options.peak.minNumOfQuantitativePeaks) |
361 -minNumOfQuantitativePeaks $peak.minNumOfQuantitativePeaks | 339 -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks |
362 #end if | 340 #end if |
363 #if str($peak.minQuantitativeIonNumber) | 341 #if str($options.peak.minQuantitativeIonNumber) |
364 -minQuantitativeIonNumber $peak.minQuantitativeIonNumber | 342 -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber |
365 #end if | 343 #end if |
366 #if str($peak.minIntensity) | 344 #if str($options.peak.minIntensity) |
367 -minIntensity $peak.minIntensity | 345 -minIntensity $options.peak.minIntensity |
368 #end if | 346 #end if |
369 #if str($peak.expectedPeakWidth) | 347 #if str($options.peak.expectedPeakWidth) |
370 -expectedPeakWidth $peak.expectedPeakWidth | 348 -expectedPeakWidth $options.peak.expectedPeakWidth |
371 #end if | 349 #end if |
372 #if $peak.filterPeaklists | 350 #if $options.peak.filterPeaklists |
373 -filterPeaklists $peak.filterPeaklists | 351 -filterPeaklists $options.peak.filterPeaklists |
374 #end if | 352 #end if |
375 #end if | 353 #end if |
376 </token> | 354 </token> |
377 | 355 |
378 <xml name="window_options"> | 356 <xml name="window_options"> |
397 </param> | 375 </param> |
398 </when> | 376 </when> |
399 </conditional> | 377 </conditional> |
400 </xml> | 378 </xml> |
401 <token name="@WINDOW_OPTIONS@"> | 379 <token name="@WINDOW_OPTIONS@"> |
402 #if $window.set_window == 'yes' | 380 #if $options.window.set_window == 'yes' |
403 #if str($window.foffset) | 381 #if str($options.window.foffset) |
404 -foffset $window.foffset | 382 -foffset $options.window.foffset |
405 #end if | 383 #end if |
406 #if str($window.poffset) | 384 #if str($options.window.poffset) |
407 -poffset $window.poffset | 385 -poffset $options.window.poffset |
408 #end if | 386 #end if |
409 #if str($window.precursorIsolationMargin) | 387 #if str($options.window.precursorIsolationMargin) |
410 -precursorIsolationMargin $window.precursorIsolationMargin | 388 -precursorIsolationMargin $options.window.precursorIsolationMargin |
411 #end if | 389 #end if |
412 #if str($window.precursorWindowSize) | 390 #if str($options.window.precursorWindowSize) |
413 -precursorWindowSize $window.precursorWindowSize | 391 -precursorWindowSize $options.window.precursorWindowSize |
414 #end if | 392 #end if |
415 #if str($window.rtWindowInMin) | 393 #if str($options.window.rtWindowInMin) |
416 -rtWindowInMin $window.rtWindowInMin | 394 -rtWindowInMin $options.window.rtWindowInMin |
417 #end if | 395 #end if |
418 #if $window.scoringBreadthType | 396 #if $options.window.scoringBreadthType |
419 -scoringBreadthType $window.scoringBreadthType | 397 -scoringBreadthType $options.window.scoringBreadthType |
420 #end if | 398 #end if |
421 #end if | 399 #end if |
422 </token> | 400 </token> |
423 | 401 |
424 <xml name="modification_options"> | 402 <xml name="modification_options"> |
443 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/> | 421 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/> |
444 </when> | 422 </when> |
445 </conditional> | 423 </conditional> |
446 </xml> | 424 </xml> |
447 <token name="@MODIFICATION_OPTIONS@"> | 425 <token name="@MODIFICATION_OPTIONS@"> |
448 #if $modifications.set_modifications == 'yes' | 426 #if $options.modifications.set_modifications == 'yes' |
449 #if $modifications.fixed | 427 #if $options.modifications.fixed |
450 -fixed $modifications.fixed | 428 -fixed $options.modifications.fixed |
451 #end if | 429 #end if |
452 -verifyModificationIons $modifications.verifyModificationIons | 430 -verifyModificationIons $options.modifications.verifyModificationIons |
453 #end if | 431 #end if |
454 </token> | 432 </token> |
455 | 433 |
456 <xml name="search_options"> | 434 <xml name="search_options"> |
457 <conditional name="search"> | 435 <conditional name="search"> |
469 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/> | 447 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/> |
470 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/> | 448 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/> |
471 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/> | 449 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/> |
472 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/> | 450 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/> |
473 <!-- | 451 <!-- |
474 <param argument="-alpha" type="float" value="1.8" min="0.0" max="5.0" label="alpha"/> | |
475 <param argument="-beta" type="float" value="0.4" min="0.0" max="5.0" label="beta"/> | |
476 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/> | 452 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/> |
477 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/> | 453 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/> |
478 --> | 454 --> |
479 </when> | 455 </when> |
480 </conditional> | 456 </conditional> |
481 </xml> | 457 </xml> |
482 <token name="@SEARCH_OPTIONS@"> | 458 <token name="@SEARCH_OPTIONS@"> |
483 #if $search.set_search == 'yes' | 459 #if $options.search.set_search == 'yes' |
484 -minCharge $search.minCharge | 460 -minCharge $options.search.minCharge |
485 -maxCharge $search.maxCharge | 461 -maxCharge $options.search.maxCharge |
486 -minLength $search.minLength | 462 -minLength $options.search.minLength |
487 -maxLength $search.maxLength | 463 -maxLength $options.search.maxLength |
488 -minEluteTime $search.minEluteTime | 464 -minEluteTime $options.search.minEluteTime |
489 -maxMissedCleavage $search.maxMissedCleavage | 465 -maxMissedCleavage $options.search.maxMissedCleavage |
490 -minQuantitativeIonNumber $search.minQuantitativeIonNumber | 466 -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber |
491 -minNumOfQuantitativePeaks $search.minNumOfQuantitativePeaks | 467 -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks |
492 -numberOfQuantitativePeaks $search.numberOfQuantitativePeaks | 468 -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks |
493 ## -alpha $search.alpha | 469 ## -addDecoysToBackground $options.search.addDecoysToBackground |
494 ## -beta $search.beta | 470 ## -dontRunDecoys $options.search.dontRunDecoys |
495 ## -addDecoysToBackground $search.addDecoysToBackground | 471 #end if |
496 ## -dontRunDecoys $search.dontRunDecoys | 472 </token> |
497 #end if | 473 |
498 </token> | 474 <xml name="options_section"> |
475 <section name="options" title="Parameter Settings" expanded="false"> | |
476 <expand macro="common_options"/> | |
477 <expand macro="mass_library_tolerance"/> | |
478 <expand macro="percolator_options"/> | |
479 <expand macro="peak_options"/> | |
480 <expand macro="window_options"/> | |
481 <expand macro="modification_options"/> | |
482 </section> | |
483 </xml> | |
484 | |
499 <xml name="libexport"> | 485 <xml name="libexport"> |
500 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/> | 486 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/> |
501 </xml> | 487 </xml> |
502 <token name="@MSCONVERT_CMD@"><![CDATA[ | 488 <token name="@MSCONVERT_CMD@"><![CDATA[ |
503 msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw | 489 msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw |