Mercurial > repos > jjohnson > encyclopedia_walnut

comparison macros.xml @ 0:925fffecea81 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
author jjohnson
date Fri, 19 Jun 2020 10:21:10 -0400
parents
children 6635b68da948
comparison
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-1:000000000000 0:925fffecea81
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 $i -l chromatogram_library.elib -f uniprot_yeast_25jan2019.fasta;
24 done
25 -->
26 <token name="@VERSION@">0.9.5</token>
27 <xml name="requirements">
28 <requirements>
29 <requirement type="package" version="@VERSION@">encyclopedia</requirement>
30 <yield/>
31 </requirements>
32 </xml>
33 <xml name="citations">
34 <citations>
35 <citation type="doi">10.1038/s41467-018-07454-w</citation>
36 <citation type="doi">10.1038/s41467-020-15346-1</citation>
37 <yield />
38 </citations>
39 </xml>
40 <token name="@CMD_IMPORTS@">
41 #import re
42 #def identifier_or_name($input1)
43 #if hasattr($input1, 'element_identifier')
44 #return $input1.element_identifier
45 #else
46 #return $input1.name
47 #end if
48 #end def
49 #def clean($name1)
50 ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i[.](fa|fasta|imzml|mzml)$)','', $re.sub('.*/','', $name1.rstrip('.gz'))))
51 ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('.*/','', $name1.rstrip('.gz')))
52 #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
53 #return $name_clean
54 #end def
55 #def ln_name($ds)
56 #set $ext = ''
57 #if $ds.is_of_type('mzml')
58 #set $ext = ".mzML"
59 #else if $ds.is_of_type('elib')
60 #set $ext = ".elib"
61 #else if $ds.is_of_type('dlib')
62 #set $ext = ".dlib"
63 #else if $ds.is_of_type('blib')
64 #set $ext = ".blib"
65 #else if $ds.is_of_type('fasta')
66 #set $ext = ".fasta"
67 #else if $ds.is_of_type('fasta.gz')
68 #set $ext = ".fasta.gz"
69 #end if
70 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
71 #return $name
72 #end def
73 #set $i_name = None
74 #set $f_name = None
75 #set $l_name = None
76 #set $t_name = None
77 </token>
78
79 <xml name="scan_input">
80 <param argument="-i" type="data" format="imzml,mzml" label="Spectrum file, .mzml or .dia"/>
81 </xml>
82 <token name="@LINK_SCAN_INPUT@"><![CDATA[
83 #set $i_name = $ln_name($i)
84 ln -s '$i' '$i_name' &&
85 ]]></token>
86 <token name="@SCAN_INPUT@">
87 -i '$i_name'
88 </token>
89
90 <xml name="scan_inputs">
91 <param argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum file, .mzml or .dia"/>
92 </xml>
93 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
94 #set $inputs_dir = 'inputs'
95 mkdir -p $inputs_dir &&
96 #for $sf in $i
97 #set $i_name = $ln_name($sf)
98 ln -s '$sf' '${inputs_dir}/${i_name}' &&
99 #end for
100 ]]></token>
101 <token name="@SCAN_INPUTS@">
102 -i '$inputs_dir'
103 </token>
104
105 <xml name="fasta_input">
106 <param argument="-f" type="data" format="fasta" label="Background protein fasta database"/>
107 </xml>
108 <token name="@LINK_FASTA_INPUT@"><![CDATA[
109 #set $f_name = $ln_name($f)
110 ln -s '$f' '$f_name' &&
111 ]]></token>
112 <token name="@FASTA_INPUT@">
113 -f '$f_name'
114 </token>
115
116 <xml name="target_fasta">
117 <param argument="-t" type="data" format="fasta" label="target FASTA file" optional="true"/>
118 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/>
119 </xml>
120 <token name="@LINK_TARGET_FASTA@"><![CDATA[
121 #if $t
122 #set $t_name = $ln_name($t)
123 ln -s '$t' '$t_name' &&
124 #else
125 #set $t_name = None
126 #end if
127 ]]></token>
128 <token name="@TARGET_FASTA@">
129 #if $t_name
130 -t '$t_name'
131 -tp $tp
132 #end if
133 </token>
134
135 <xml name="lib_input" token_optional="true" token_help="">
136 <param argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB">
137 <help>@HELP@</help>
138 </param>
139 </xml>
140 <token name="@LINK_LIB_INPUT@"><![CDATA[
141 #if $l
142 #set $l_name = $ln_name($l)
143 cp '$l' $l_name &&
144 #else
145 #set $l_name = None
146 #end if
147 ]]></token>
148 <token name="@LIB_INPUT@">
149 #if $l_name
150 -l '$l_name'
151 #end if
152 </token>
153
154 <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false"
155 token_cid_selected="false" token_hcd_selected="false">
156 <conditional name="acquisition">
157 <param name="set_acquisition" type="select" label="Set Acquisition Options">
158 <option value="no">No - use default options</option>
159 <option value="yes">Yes</option>
160 </param>
161 <when value="no"/>
162 <when value="yes">
163 <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/>
164 <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type">
165 <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option>
166 <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option>
167 </param>
168 <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme">
169 <option value="Trypsin">Trypsin</option>
170 <option value="Trypsin/p">Trypsin/p</option>
171 <option value="Lys-C">Lys-C</option>
172 <option value="Lys-N">Lys-N</option>
173 <option value="Arg-C">Arg-C</option>
174 <option value="Glu-C">Glu-C</option>
175 <option value="Chymotrypsin">Chymotrypsin</option>
176 <option value="Pepsin A">Pepsin A</option>
177 <option value="Elastase">Elastase</option>
178 <option value="Thermolysin">Thermolysin</option>
179 <option value="No Enzyme">No Enzyme</option>
180 </param>
181 <param argument="-frag" type="select" optional="true" label="Fragmentation">
182 <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option>
183 <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option>
184 <option value="ETD">ETD (C/Z/Z+1)</option>
185 </param>
186 </when>
187 </conditional>
188 </xml>
189 <xml name="encyclopedia_common_options">
190 <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false"
191 token_cid_selected="true" token_hcd_selected="false"/>
192 </xml>
193 <xml name="walnut_common_options">
194 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true"
195 token_cid_selected="false" token_hcd_selected="true"/>
196 </xml>
197 <token name="@COMMON_OPTIONS@">
198 #if $acquisition.set_acquisition == 'yes'
199 -numberOfExtraDecoyLibrariesSearched $acquisition.numberOfExtraDecoyLibrariesSearched
200 #if $acquisition.acquisition
201 -acquisition '$acquisition.acquisition'
202 #end if
203 #if $acquisition.enzyme:
204 -enzyme '$acquisition.enzyme'
205 #end if
206 #if $acquisition.frag:
207 -frag '$acquisition.frag'
208 #end if
209 #end if
210 </token>
211
212 <xml name="mass_tolerance">
213 <conditional name="tolerance">
214 <param name="set_tolerance" type="select" label="Set Tolerance Options">
215 <option value="no">No - use default options</option>
216 <option value="yes">Yes</option>
217 </param>
218 <when value="no"/>
219 <when value="yes">
220 <conditional name="precursor_tolerance">
221 <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance">
222 <option value="PPM">PPM</option>
223 <option value="AMU">AMU</option>
224 <option value="Resolution">Resolution</option>
225 </param>
226 <when value="PPM">
227 <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/>
228 </when>
229 <when value="AMU">
230 <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/>
231 </when>
232 <when value="Resolution">
233 <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/>
234 </when>
235 </conditional>
236 <conditional name="fragment_tolerance">
237 <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance">
238 <option value="PPM">PPM</option>
239 <option value="AMU">AMU</option>
240 <option value="Resolution">Resolution</option>
241 </param>
242 <when value="PPM">
243 <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/>
244 </when>
245 <when value="AMU">
246 <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/>
247 </when>
248 <when value="Resolution">
249 <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/>
250 </when>
251 </conditional>
252 <yield/>
253 </when>
254 </conditional>
255 </xml>
256 <token name="@MASS_TOLERANCE@">
257 #if $tolerance.set_tolerance == 'yes'
258 -ptolunits $tolerance.precursor_tolerance.ptolunits
259 -ptol $tolerance.precursor_tolerance.ptol
260 -ftolunits $tolerance.fragment_tolerance.ftolunits
261 -ftol $tolerance.fragment_tolerance.ftol
262 #end if
263 </token>
264
265 <xml name="mass_library_tolerance">
266 <expand macro="mass_tolerance">
267 <conditional name="library_tolerance">
268 <param argument="-ltolunits" type="select" label="Library Mass Tolerance">
269 <option value="defaults">Use defaults</option>
270 <option value="PPM">PPM</option>
271 <option value="AMU">AMU</option>
272 <option value="Resolution">Resolution</option>
273 </param>
274 <when value="defaults"/>
275 <when value="PPM">
276 <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/>
277 </when>
278 <when value="AMU">
279 <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/>
280 </when>
281 <when value="Resolution">
282 <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/>
283 </when>
284 </conditional>
285 </expand>
286 </xml>
287 <token name="@MASS_LIBRARY_TOLERANCE@">
288 @MASS_TOLERANCE@
289 #if $tolerance.set_tolerance == 'yes' and $tolerance.library_tolerance.ltolunits != 'defaults'
290 -ltolunits $tolerance.library_tolerance.ltolunits
291 -ltol $tolerance.library_tolerance.ltol
292 #end if
293 </token>
294
295 <xml name="percolator_options">
296 <conditional name="percolator">
297 <param name="set_percolator" type="select" label="Set Percolator Options">
298 <option value="no">No - use default options</option>
299 <option value="yes">Yes</option>
300 </param>
301 <when value="no"/>
302 <when value="yes">
303 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
304 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
305 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
306 </when>
307 </conditional>
308 </xml>
309 <token name="@PERCOLATOR_OPTIONS@">
310 #if $percolator.set_percolator == 'yes'
311 #if str($percolator.percolatorVersionNumber)
312 -percolatorVersionNumber $percolator.percolatorVersionNumber
313 #end if
314 #if str($percolator.percolatorProteinThreshold)
315 -percolatorProteinThreshold $percolator.percolatorProteinThreshold
316 #end if
317 #if str($percolator.percolatorThreshold)
318 -percolatorThreshold $percolator.percolatorThreshold
319 #end if
320 #end if
321 </token>
322
323 <xml name="peak_options">
324 <conditional name="peak">
325 <param name="set_peak" type="select" label="Set Peak Options">
326 <option value="no">No - use default options</option>
327 <option value="yes">Yes</option>
328 </param>
329 <when value="no"/>
330 <when value="yes">
331 <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/>
332 <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/>
333 <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/>
334 <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/>
335 <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/>
336 <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists">
337 <option value="false">No</option>
338 <option value="true">Yes</option>
339 </param>
340 </when>
341 </conditional>
342 </xml>
343 <token name="@PEAK_OPTIONS@">
344 #if $peak.set_peak == 'yes'
345 #if str($peak.numberOfQuantitativePeaks)
346 -numberOfQuantitativePeaks $peak.numberOfQuantitativePeaks
347 #end if
348 #if str($peak.minNumOfQuantitativePeaks)
349 -minNumOfQuantitativePeaks $peak.minNumOfQuantitativePeaks
350 #end if
351 #if str($peak.minQuantitativeIonNumber)
352 -minQuantitativeIonNumber $peak.minQuantitativeIonNumber
353 #end if
354 #if str($peak.minIntensity)
355 -minIntensity $peak.minIntensity
356 #end if
357 #if str($peak.expectedPeakWidth)
358 -expectedPeakWidth $peak.expectedPeakWidth
359 #end if
360 #if $peak.filterPeaklists
361 -filterPeaklists $peak.filterPeaklists
362 #end if
363 #end if
364 </token>
365
366 <xml name="window_options">
367 <conditional name="window">
368 <param name="set_window" type="select" label="Set Window Options">
369 <option value="no">No - use default options</option>
370 <option value="yes">Yes</option>
371 </param>
372 <when value="no"/>
373 <when value="yes">
374 <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/>
375 <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/>
376 <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/>
377 <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/>
378 <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/>
379 <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType">
380 <option value="window">Across entire window</option>
381 <option value="recal20">Recalibrated (20% gradient)</option>
382 <option value="recal">Recalibrated (peak width only)</option>
383 <option value="uncal20">Uncalibrated (20% gradient)</option>
384 <option value="uncal">Uncalibrated (peak width only)</option>
385 </param>
386 </when>
387 </conditional>
388 </xml>
389 <token name="@WINDOW_OPTIONS@">
390 #if $window.set_window == 'yes'
391 #if str($window.foffset)
392 -foffset $window.foffset
393 #end if
394 #if str($window.poffset)
395 -poffset $window.poffset
396 #end if
397 #if str($window.precursorIsolationMargin)
398 -precursorIsolationMargin $window.precursorIsolationMargin
399 #end if
400 #if str($window.precursorWindowSize)
401 -precursorWindowSize $window.precursorWindowSize
402 #end if
403 #if str($window.rtWindowInMin)
404 -rtWindowInMin $window.rtWindowInMin
405 #end if
406 #if $window.scoringBreadthType
407 -scoringBreadthType $window.scoringBreadthType
408 #end if
409 #end if
410 </token>
411
412 <xml name="modification_options">
413 <conditional name="modifications">
414 <param name="set_modifications" type="select" label="Set Modifications Options">
415 <option value="no">No - use default options</option>
416 <option value="yes">Yes</option>
417 </param>
418 <when value="no"/>
419 <when value="yes">
420 <param argument="-fixed" type="select" optional="true" label="Fixed Modification">
421 <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option>
422 <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option>
423 <option value="C=45.987721">C+46 (MMTS) C=45.987721</option>
424 <option value="C=125.047679">C+125 (NEM) C=125.047679</option>
425 </param>
426 <yield/>
427 <!--
428 <param argument="-localizationModification" type="select" optional="true" label="localizationModification">
429 </param>
430 -->
431 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/>
432 </when>
433 </conditional>
434 </xml>
435 <token name="@MODIFICATION_OPTIONS@">
436 #if $modifications.set_modifications == 'yes'
437 #if $modifications.fixed
438 -fixed $modifications.fixed
439 #end if
440 -verifyModificationIons $modifications.verifyModificationIons
441 #end if
442 </token>
443
444 <xml name="search_options">
445 <conditional name="search">
446 <param name="set_search" type="select" label="Set Search Options">
447 <option value="no">No - use default options</option>
448 <option value="yes">Yes</option>
449 </param>
450 <when value="no"/>
451 <when value="yes">
452 <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/>
453 <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/>
454 <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/>
455 <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/>
456 <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/>
457 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/>
458 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/>
459 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/>
460 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>
461 <!--
462 <param argument="-alpha" type="float" value="1.8" min="0.0" max="5.0" label="alpha"/>
463 <param argument="-beta" type="float" value="0.4" min="0.0" max="5.0" label="beta"/>
464 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/>
465 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>
466 -->
467 </when>
468 </conditional>
469 </xml>
470 <token name="@SEARCH_OPTIONS@">
471 #if $search.set_search == 'yes'
472 -minCharge $search.minCharge
473 -maxCharge $search.maxCharge
474 -minLength $search.minLength
475 -maxLength $search.maxLength
476 -minEluteTime $search.minEluteTime
477 -maxMissedCleavage $search.maxMissedCleavage
478 -minQuantitativeIonNumber $search.minQuantitativeIonNumber
479 -minNumOfQuantitativePeaks $search.minNumOfQuantitativePeaks
480 -numberOfQuantitativePeaks $search.numberOfQuantitativePeaks
481 ## -alpha $search.alpha
482 ## -beta $search.beta
483 ## -addDecoysToBackground $search.addDecoysToBackground
484 ## -dontRunDecoys $search.dontRunDecoys
485 #end if
486 </token>
487 <!--
488 minNumOfQuantitativePeaks minQuantitativeIonNumber numberOfQuantitativePeaks numberOfReportedPeaksu
489 +acquisition (default: overlapping dia)
490 +addDecoysToBackground (default: false)
491 +alpha (default: 1.8)
492 +beta (default: 0.4)
493 +dontRunDecoys (default: false)
494 +enzyme (default: trypsin)
495 +filterPeaklists (default: false)
496 +fixed (default: C=57.0214635)
497 +foffset (default: 0)
498 =frag (default: YONLY)
499 +ftol (default: 10)
500 +ftolunits (default: ppm)
501 +maxCharge (default: 3)
502 +ftolunits (default: ppm)
503 +maxCharge (default: 3)
504 +maxLength (default: 100)
505 +maxMissedCleavage (default: 1)
506 +minCharge (default: 2)
507 +minEluteTime (default: 12)
508 +minIntensity (default: -1.0)
509 +minLength (default: 5)
510 +minNumOfQuantitativePeaks (default: 3)
511 +minQuantitativeIonNumber (default: 3)
512 +numberOfQuantitativePeaks (default: 5)
513 -numberOfReportedPeaks (default: 1)
514 -numberOfThreadsUsed (default: 12)
515 +percolatorProteinThreshol (default: 0.01)
516 +percolatorThreshold (default: 0.01)
517 +percolatorVersionNumber (default: 3)
518 +poffset (default: 0)
519 +precursorIsolationMargin (default: 0)
520 +precursorWindowSize (default: -1)
521 +ptol (default: 10)
522 +ptolunits (default: ppm)
523 -requireVariableMods (default: false)
524 -variable (default: -)
525 -->
526 <xml name="libexport">
527 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/>
528 </xml>
529 </macros>
530 <!--
531 e w t x l param
532 +:+:+:+:+ i
533 +:+:+:+:+ l
534 +:+:+:+:+ f
535
536 +:+:+:+:+ t
537 -:+:-:+:- tp
538 -:+:-:+:+ a
539
540 +:+:+:+:+ o
541
542 +:+:+:+:- acquisition
543 -:+:-:+:- addDecoysToBackground
544 -:+:-:+:- alpha
545 -:+:-:+:- beta
546 -:-:-:-:+ blib
547 -:+:-:+:- dontRunDecoys
548 +:+:+:+:- enzyme
549 +:-:+:-:- expectedPeakWidth
550 +:+:+:+:- filterPeaklists
551 +:+:+:+:+ fixed
552 +:+:+:+:+ foffset
553 +:+:+:+:- frag
554 +:+:+:+:+ ftol
555 +:+:+:+:+ ftolunits
556 +:-:+:-:- lftol
557 +:-:+:-:- lftolunits
558 +:-:-:-:- libexport
559 +:-:+:-:+ localizationModification
560 -:+:-:+:- maxCharge
561 -:+:-:+:- maxLength
562 -:+:-:+:- maxMissedCleavage
563 -:+:-:+:- minCharge
564 -:+:-:+:- minEluteTime
565 +:+:+:+:- minIntensity
566 -:+:-:+:- minLength
567 +:+:+:+:+ minNumOfQuantitativePeaks
568 +:+:+:+:+ minQuantitativeIonNumber
569 +:-:+:-:+ numberOfExtraDecoyLibrariesSearched
570 +:+:+:+:+ numberOfQuantitativePeaks
571 -:+:-:+:- numberOfReportedPeaks
572 -:+:-:+:- numberOfThreadsUsed
573 -:-:-:-:+ percolatorLocation
574 -:+:-:+:- percolatorProteinThreshol
575 +:-:+:-:+ percolatorProteinThreshold
576 +:+:+:+:+ percolatorThreshold
577 +:+:+:+:- percolatorVersionNumber
578 -:-:-:-:+ phospho
579 +:+:+:+:- poffset
580 +:+:+:+:- precursorIsolationMargin
581 +:+:+:+:- precursorWindowSize
582 +:+:+:+:- ptol
583 +:+:+:+:- ptolunits
584 -:+:-:+:- requireVariableMods
585 +:-:+:-:- rtWindowInMin
586 +:-:+:-:- scoringBreadthType
587 -:+:-:+:- variable
588 +:-:+:-:- verifyModificationIons
589 -->