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comparison macros.xml @ 0:8a9cef108b0c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
author galaxyp
date Mon, 14 Sep 2020 17:06:37 +0000
parents
children 0e25453fbee7
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-1:000000000000 0:8a9cef108b0c
1 <macros>
2 <token name="@VERSION@">0.9.5</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@VERSION@">encyclopedia</requirement>
6 <yield/>
7 </requirements>
8 </xml>
9
10 <token name="@ENCYCLOPEDIA_WIKI@">
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. See: https://bitbucket.org/searleb/encyclopedia/wiki/Home
12
13 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home
14 </token>
15 <xml name="citations">
16 <citations>
17 <citation type="doi">10.1038/s41467-018-07454-w</citation>
18 <citation type="doi">10.1038/s41467-020-15346-1</citation>
19 <citation type="doi">10.1074/mcp.P119.001913</citation>
20 <yield/>
21 </citations>
22 </xml>
23
24 <token name="@CMD_IMPORTS@">
25 #import re
26 #def identifier_or_name($input1)
27 #if hasattr($input1, 'element_identifier')
28 #return $input1.element_identifier
29 #else
30 #return $input1.name
31 #end if
32 #end def
33 #def clean($name1)
34 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
35 #return $name_clean
36 #end def
37 #def ln_name($ds)
38 #set $ext = ''
39 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
40 #set $ext = ".mzML"
41 #else if $ds.is_of_type('elib')
42 #set $ext = ".elib"
43 #else if $ds.is_of_type('dlib')
44 #set $ext = ".dlib"
45 #else if $ds.is_of_type('blib')
46 #set $ext = ".blib"
47 #else if $ds.is_of_type('fasta')
48 #set $ext = ".fasta"
49 #else if $ds.is_of_type('fasta.gz')
50 #set $ext = ".fasta.gz"
51 #end if
52 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
53 #return $name
54 #end def
55 #set $i_name = None
56 #set $f_name = None
57 #set $l_name = None
58 #set $t_name = None
59 </token>
60
61 <xml name="scan_input">
62 <param name="scan_input" argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format">
63 <help>@MSCONVERT_RAW@</help>
64 </param>
65 </xml>
66 <token name="@LINK_SCAN_INPUT@"><![CDATA[
67 #set $i_name = $ln_name($scan_input)
68 ln -s '$scan_input' '$i_name' &&
69 ]]></token>
70 <token name="@SCAN_INPUT@">
71 -i '$i_name'
72 </token>
73
74 <xml name="scan_inputs">
75 <param name="scan_inputs" argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format">
76 <help>@MSCONVERT_RAW@</help>
77 </param>
78 </xml>
79 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
80 #set $inputs_dir = 'inputs'
81 mkdir -p $inputs_dir &&
82 #for $sf in $scan_inputs
83 #set $i_name = $ln_name($sf)
84 ln -s '$sf' '${inputs_dir}/${i_name}' &&
85 #end for
86 ]]></token>
87 <token name="@SCAN_INPUTS@">
88 -i '$inputs_dir'
89 </token>
90
91 <xml name="fasta_input">
92 <param name="fasta" argument="-f" type="data" format="fasta" label="Background proteome protein fasta database">
93 <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help>
94 </param>
95 </xml>
96 <token name="@LINK_FASTA_INPUT@"><![CDATA[
97 #set $f_name = $ln_name($fasta)
98 ln -s '$fasta' '$f_name' &&
99 ]]></token>
100 <token name="@FASTA_INPUT@">
101 -f '$f_name'
102 </token>
103
104 <xml name="target_fasta">
105 <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true">
106 <help>Optional - Only analyze this subset of the background fasta proteome</help>
107 </param>
108 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Target FASTA file contains peptides">
109 <help>Rather than full proteins</help>
110 </param>
111 </xml>
112 <token name="@LINK_TARGET_FASTA@"><![CDATA[
113 #if $target_fasta
114 #set $t_name = $ln_name($target_fasta)
115 ln -s '$target_fasta' '$t_name' &&
116 #else
117 #set $t_name = None
118 #end if
119 ]]></token>
120 <token name="@TARGET_FASTA@">
121 #if $t_name
122 -t '$t_name'
123 -tp $tp
124 #end if
125 </token>
126
127 <xml name="lib_input" token_optional="true" token_libhelp="">
128 <param name="library" argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB">
129 <help>@LIBHELP@</help>
130 </param>
131 </xml>
132 <token name="@LINK_LIB_INPUT@"><![CDATA[
133 #if $library
134 #set $l_name = $ln_name($library)
135 cp '$library' '$l_name' &&
136 #else
137 #set $l_name = None
138 #end if
139 ]]></token>
140 <token name="@LIB_INPUT@">
141 #if $l_name
142 -l '$l_name'
143 #end if
144 </token>
145
146 <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false"
147 token_cid_selected="false" token_hcd_selected="false">
148 <conditional name="acquisition">
149 <param name="set_acquisition" type="select" label="Set Acquisition Options">
150 <option value="no">No - use default options</option>
151 <option value="yes">Yes</option>
152 </param>
153 <when value="no"/>
154 <when value="yes">
155 <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/>
156 <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type">
157 <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option>
158 <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option>
159 </param>
160 <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme">
161 <option value="Trypsin">Trypsin</option>
162 <option value="Trypsin/p">Trypsin/p</option>
163 <option value="Lys-C">Lys-C</option>
164 <option value="Lys-N">Lys-N</option>
165 <option value="Arg-C">Arg-C</option>
166 <option value="Glu-C">Glu-C</option>
167 <option value="Chymotrypsin">Chymotrypsin</option>
168 <option value="Pepsin A">Pepsin A</option>
169 <option value="Elastase">Elastase</option>
170 <option value="Thermolysin">Thermolysin</option>
171 <option value="No Enzyme">No Enzyme</option>
172 </param>
173 <param argument="-frag" type="select" optional="true" label="Fragmentation">
174 <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option>
175 <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option>
176 <option value="ETD">ETD (C/Z/Z+1)</option>
177 </param>
178 </when>
179 </conditional>
180 </xml>
181 <xml name="encyclopedia_common_options">
182 <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false"
183 token_cid_selected="true" token_hcd_selected="false"/>
184 </xml>
185 <xml name="walnut_common_options">
186 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true"
187 token_cid_selected="false" token_hcd_selected="true"/>
188 </xml>
189 <token name="@COMMON_OPTIONS@">
190 #if $options.acquisition.set_acquisition == 'yes'
191 -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched
192 #if $options.acquisition.acquisition
193 -acquisition '$options.acquisition.acquisition'
194 #end if
195 #if $options.acquisition.enzyme:
196 -enzyme '$options.acquisition.enzyme'
197 #end if
198 #if $options.acquisition.frag:
199 -frag '$options.acquisition.frag'
200 #end if
201 #end if
202 </token>
203
204 <xml name="mass_tolerance">
205 <conditional name="tolerance">
206 <param name="set_tolerance" type="select" label="Set Tolerance Options">
207 <option value="no">No - use default options</option>
208 <option value="yes">Yes</option>
209 </param>
210 <when value="no"/>
211 <when value="yes">
212 <conditional name="precursor_tolerance">
213 <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance">
214 <option value="PPM">PPM</option>
215 <option value="AMU">AMU</option>
216 <option value="Resolution">Resolution</option>
217 </param>
218 <when value="PPM">
219 <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/>
220 </when>
221 <when value="AMU">
222 <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/>
223 </when>
224 <when value="Resolution">
225 <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/>
226 </when>
227 </conditional>
228 <conditional name="fragment_tolerance">
229 <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance">
230 <option value="PPM">PPM</option>
231 <option value="AMU">AMU</option>
232 <option value="Resolution">Resolution</option>
233 </param>
234 <when value="PPM">
235 <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/>
236 </when>
237 <when value="AMU">
238 <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/>
239 </when>
240 <when value="Resolution">
241 <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/>
242 </when>
243 </conditional>
244 <yield/>
245 </when>
246 </conditional>
247 </xml>
248 <token name="@MASS_TOLERANCE@">
249 #if $options.tolerance.set_tolerance == 'yes'
250 -ptolunits $options.tolerance.precursor_tolerance.ptolunits
251 -ptol $options.tolerance.precursor_tolerance.ptol
252 -ftolunits $options.tolerance.fragment_tolerance.ftolunits
253 -ftol $options.tolerance.fragment_tolerance.ftol
254 #end if
255 </token>
256
257 <xml name="mass_library_tolerance">
258 <expand macro="mass_tolerance">
259 <conditional name="library_tolerance">
260 <param argument="-ltolunits" type="select" label="Library Mass Tolerance">
261 <option value="defaults">Use defaults</option>
262 <option value="PPM">PPM</option>
263 <option value="AMU">AMU</option>
264 <option value="Resolution">Resolution</option>
265 </param>
266 <when value="defaults"/>
267 <when value="PPM">
268 <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/>
269 </when>
270 <when value="AMU">
271 <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/>
272 </when>
273 <when value="Resolution">
274 <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/>
275 </when>
276 </conditional>
277 </expand>
278 </xml>
279 <token name="@MASS_LIBRARY_TOLERANCE@">
280 @MASS_TOLERANCE@
281 #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults'
282 -ltolunits $options.tolerance.library_tolerance.ltolunits
283 -ltol $options.tolerance.library_tolerance.ltol
284 #end if
285 </token>
286
287 <xml name="percolator_options">
288 <conditional name="percolator">
289 <param name="set_percolator" type="select" label="Set Percolator Options">
290 <option value="no">No - use default options</option>
291 <option value="yes">Yes</option>
292 </param>
293 <when value="no"/>
294 <when value="yes">
295 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
296 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
297 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
298 </when>
299 </conditional>
300 </xml>
301 <token name="@PERCOLATOR_OPTIONS@">
302 #if $options.percolator.set_percolator == 'yes'
303 #if str($options.percolator.percolatorVersionNumber)
304 -percolatorVersionNumber $options.percolator.percolatorVersionNumber
305 #end if
306 #if str($options.percolator.percolatorProteinThreshold)
307 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
308 #end if
309 #if str($options.percolator.percolatorThreshold)
310 -percolatorThreshold $options.percolator.percolatorThreshold
311 #end if
312 #end if
313 </token>
314
315 <xml name="peak_options">
316 <conditional name="peak">
317 <param name="set_peak" type="select" label="Set Peak Options">
318 <option value="no">No - use default options</option>
319 <option value="yes">Yes</option>
320 </param>
321 <when value="no"/>
322 <when value="yes">
323 <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/>
324 <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/>
325 <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/>
326 <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/>
327 <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/>
328 <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists">
329 <option value="false">No</option>
330 <option value="true">Yes</option>
331 </param>
332 </when>
333 </conditional>
334 </xml>
335 <token name="@PEAK_OPTIONS@">
336 #if $options.peak.set_peak == 'yes'
337 #if str($options.peak.numberOfQuantitativePeaks)
338 -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks
339 #end if
340 #if str($options.peak.minNumOfQuantitativePeaks)
341 -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks
342 #end if
343 #if str($options.peak.minQuantitativeIonNumber)
344 -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber
345 #end if
346 #if str($options.peak.minIntensity)
347 -minIntensity $options.peak.minIntensity
348 #end if
349 #if str($options.peak.expectedPeakWidth)
350 -expectedPeakWidth $options.peak.expectedPeakWidth
351 #end if
352 #if $options.peak.filterPeaklists
353 -filterPeaklists $options.peak.filterPeaklists
354 #end if
355 #end if
356 </token>
357
358 <xml name="window_options">
359 <conditional name="window">
360 <param name="set_window" type="select" label="Set Window Options">
361 <option value="no">No - use default options</option>
362 <option value="yes">Yes</option>
363 </param>
364 <when value="no"/>
365 <when value="yes">
366 <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/>
367 <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/>
368 <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/>
369 <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/>
370 <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/>
371 <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType">
372 <option value="window">Across entire window</option>
373 <option value="recal20">Recalibrated (20% gradient)</option>
374 <option value="recal">Recalibrated (peak width only)</option>
375 <option value="uncal20">Uncalibrated (20% gradient)</option>
376 <option value="uncal">Uncalibrated (peak width only)</option>
377 </param>
378 </when>
379 </conditional>
380 </xml>
381 <token name="@WINDOW_OPTIONS@">
382 #if $options.window.set_window == 'yes'
383 #if str($options.window.foffset)
384 -foffset $options.window.foffset
385 #end if
386 #if str($options.window.poffset)
387 -poffset $options.window.poffset
388 #end if
389 #if str($options.window.precursorIsolationMargin)
390 -precursorIsolationMargin $options.window.precursorIsolationMargin
391 #end if
392 #if str($options.window.precursorWindowSize)
393 -precursorWindowSize $options.window.precursorWindowSize
394 #end if
395 #if str($options.window.rtWindowInMin)
396 -rtWindowInMin $options.window.rtWindowInMin
397 #end if
398 #if $options.window.scoringBreadthType
399 -scoringBreadthType $options.window.scoringBreadthType
400 #end if
401 #end if
402 </token>
403
404 <xml name="modification_options">
405 <conditional name="modifications">
406 <param name="set_modifications" type="select" label="Set Modifications Options">
407 <option value="no">No - use default options</option>
408 <option value="yes">Yes</option>
409 </param>
410 <when value="no"/>
411 <when value="yes">
412 <param argument="-fixed" type="select" optional="true" label="Fixed Modification">
413 <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option>
414 <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option>
415 <option value="C=45.987721">C+46 (MMTS) C=45.987721</option>
416 <option value="C=125.047679">C+125 (NEM) C=125.047679</option>
417 </param>
418 <yield/>
419 <!--
420 <param argument="-localizationModification" type="select" optional="true" label="localizationModification">
421 </param>
422 -->
423 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/>
424 </when>
425 </conditional>
426 </xml>
427 <token name="@MODIFICATION_OPTIONS@">
428 #if $options.modifications.set_modifications == 'yes'
429 #if $options.modifications.fixed
430 -fixed $options.modifications.fixed
431 #end if
432 -verifyModificationIons $options.modifications.verifyModificationIons
433 #end if
434 </token>
435
436 <xml name="search_options">
437 <conditional name="search">
438 <param name="set_search" type="select" label="Set Search Options">
439 <option value="no">No - use default options</option>
440 <option value="yes">Yes</option>
441 </param>
442 <when value="no"/>
443 <when value="yes">
444 <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/>
445 <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/>
446 <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/>
447 <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/>
448 <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/>
449 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/>
450 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/>
451 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/>
452 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>
453 <!--
454 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/>
455 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>
456 -->
457 </when>
458 </conditional>
459 </xml>
460 <token name="@SEARCH_OPTIONS@">
461 #if $options.search.set_search == 'yes'
462 -minCharge $options.search.minCharge
463 -maxCharge $options.search.maxCharge
464 -minLength $options.search.minLength
465 -maxLength $options.search.maxLength
466 -minEluteTime $options.search.minEluteTime
467 -maxMissedCleavage $options.search.maxMissedCleavage
468 -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber
469 -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks
470 -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks
471 ## -addDecoysToBackground $options.search.addDecoysToBackground
472 ## -dontRunDecoys $options.search.dontRunDecoys
473 #end if
474 </token>
475
476 <xml name="options_section">
477 <section name="options" title="Parameter Settings" expanded="false">
478 <expand macro="common_options"/>
479 <expand macro="mass_library_tolerance"/>
480 <expand macro="percolator_options"/>
481 <expand macro="peak_options"/>
482 <expand macro="window_options"/>
483 <expand macro="modification_options"/>
484 <expand macro="search_options"/>
485 </section>
486 </xml>
487
488 <xml name="libexport">
489 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/>
490 </xml>
491
492 <token name="@SEARCH2LIB_CMDS@"><![CDATA[
493 @CMD_IMPORTS@
494 @LINK_SCAN_INPUTS@
495 @LINK_FASTA_INPUT@
496 @LINK_TARGET_FASTA@
497 @LINK_LIB_INPUT@
498 for SCAN_FILE in `ls -1 inputs/*`; do
499 echo "\$SCAN_FILE" &&
500 EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
501 -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g
502 -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
503 #if not $library
504 -walnut
505 #end if
506 -i \$SCAN_FILE
507 @FASTA_INPUT@
508 @TARGET_FASTA@
509 @LIB_INPUT@
510 @COMMON_OPTIONS@
511 @MASS_LIBRARY_TOLERANCE@
512 @PERCOLATOR_OPTIONS@
513 @PEAK_OPTIONS@
514 @WINDOW_OPTIONS@
515 @MODIFICATION_OPTIONS@
516 @SEARCH_OPTIONS@ | tee -a search2lib.log
517 ; done &&
518 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
519 EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport
520 #if not $library
521 -pecan
522 #end if
523 @SCAN_INPUTS@
524 @FASTA_INPUT@
525 @TARGET_FASTA@
526 @LIB_INPUT@
527 -a $a
528 -o chromatogram_library.elib
529 && ls -l ./*.* inputs/*
530 | tee -a search2lib.log
531 ]]>
532 </token>
533 <token name="@MSCONVERT_CMD@"><![CDATA[
534 msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw
535 ]]>
536 </token>
537 <token name="@MSCONVERT_RAW@"><![CDATA[
538 mzML conversion from RAW requires special options: @MSCONVERT_CMD@
539 ]]>
540 </token>
541 <token name="@MSCONVERT_HELP@"><![CDATA[
542
543 The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options:
544
545 ::
546
547 @MSCONVERT_CMD@
548
549 ]]>
550 </token>
551 </macros>