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comparison macros.xml @ 2:114b44e35d30 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
author jjohnson
date Wed, 01 Jul 2020 11:24:59 -0400
parents 6635b68da948
children e37e3c4a87a9
comparison
equal deleted inserted replaced
1:6635b68da948 2:114b44e35d30
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