Mercurial > repos > galaxyp > encyclopedia_quantify
comparison macros.xml @ 0:4081e4faa4ab draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
author | galaxyp |
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date | Mon, 14 Sep 2020 17:06:06 +0000 |
parents | |
children | 1c5cbf8f79ce |
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-1:000000000000 | 0:4081e4faa4ab |
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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> |