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comparison macros.xml @ 1:d44902652df2 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 16:58:35 +0000
parents 9002bb1c248d
children b641a320fcc8
comparison
equal deleted inserted replaced
0:9002bb1c248d 1:d44902652df2
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 $i -l chromatogram_library.elib -f uniprot_yeast_25jan2019.fasta;
24 done
25 -->
26 <token name="@VERSION@">0.9.5</token> 2 <token name="@VERSION@">0.9.5</token>
27 <xml name="requirements"> 3 <xml name="requirements">
28 <requirements> 4 <requirements>
29 <requirement type="package" version="@VERSION@">encyclopedia</requirement> 5 <requirement type="package" version="@VERSION@">encyclopedia</requirement>
30 <yield/> 6 <yield/>
31 </requirements> 7 </requirements>
32 </xml> 8 </xml>
9
10 <token name="@ENCYCLOPEDIA_WIKI@">
11 EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. See: https://bitbucket.org/searleb/encyclopedia/wiki/Home
12
13 .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home
14 </token>
33 <xml name="citations"> 15 <xml name="citations">
34 <citations> 16 <citations>
35 <citation type="doi">10.1038/s41467-018-07454-w</citation> 17 <citation type="doi">10.1038/s41467-018-07454-w</citation>
36 <citation type="doi">10.1038/s41467-020-15346-1</citation> 18 <citation type="doi">10.1038/s41467-020-15346-1</citation>
37 <yield /> 19 <citation type="doi">10.1074/mcp.P119.001913</citation>
20 <yield/>
38 </citations> 21 </citations>
39 </xml> 22 </xml>
23
40 <token name="@CMD_IMPORTS@"> 24 <token name="@CMD_IMPORTS@">
41 #import re 25 #import re
42 #def identifier_or_name($input1) 26 #def identifier_or_name($input1)
43 #if hasattr($input1, 'element_identifier') 27 #if hasattr($input1, 'element_identifier')
44 #return $input1.element_identifier 28 #return $input1.element_identifier
45 #else 29 #else
46 #return $input1.name 30 #return $input1.name
47 #end if 31 #end if
48 #end def 32 #end def
49 #def clean($name1) 33 #def clean($name1)
50 ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i[.](fa|fasta|imzml|mzml)$)','', $re.sub('.*/','', $name1.rstrip('.gz')))) 34 #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 35 #return $name_clean
54 #end def 36 #end def
55 #def ln_name($ds) 37 #def ln_name($ds)
56 #set $ext = '' 38 #set $ext = ''
57 #if $ds.is_of_type('mzml') 39 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
58 #set $ext = ".mzML" 40 #set $ext = ".mzML"
59 #else if $ds.is_of_type('elib') 41 #else if $ds.is_of_type('elib')
60 #set $ext = ".elib" 42 #set $ext = ".elib"
61 #else if $ds.is_of_type('dlib') 43 #else if $ds.is_of_type('dlib')
62 #set $ext = ".dlib" 44 #set $ext = ".dlib"
75 #set $l_name = None 57 #set $l_name = None
76 #set $t_name = None 58 #set $t_name = None
77 </token> 59 </token>
78 60
79 <xml name="scan_input"> 61 <xml name="scan_input">
80 <param argument="-i" type="data" format="imzml,mzml" label="Spectrum file, .mzml or .dia"/> 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>
81 </xml> 65 </xml>
82 <token name="@LINK_SCAN_INPUT@"><![CDATA[ 66 <token name="@LINK_SCAN_INPUT@"><![CDATA[
83 #set $i_name = $ln_name($i) 67 #set $i_name = $ln_name($scan_input)
84 ln -s '$i' '$i_name' && 68 ln -s '$scan_input' '$i_name' &&
85 ]]></token> 69 ]]></token>
86 <token name="@SCAN_INPUT@"> 70 <token name="@SCAN_INPUT@">
87 -i '$i_name' 71 -i '$i_name'
88 </token> 72 </token>
89 73
90 <xml name="scan_inputs"> 74 <xml name="scan_inputs">
91 <param argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum file, .mzml or .dia"/> 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>
92 </xml> 78 </xml>
93 <token name="@LINK_SCAN_INPUTS@"><![CDATA[ 79 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
94 #set $inputs_dir = 'inputs' 80 #set $inputs_dir = 'inputs'
95 mkdir -p $inputs_dir && 81 mkdir -p $inputs_dir &&
96 #for $sf in $i 82 #for $sf in $scan_inputs
97 #set $i_name = $ln_name($sf) 83 #set $i_name = $ln_name($sf)
98 ln -s '$sf' '${inputs_dir}/${i_name}' && 84 ln -s '$sf' '${inputs_dir}/${i_name}' &&
99 #end for 85 #end for
100 ]]></token> 86 ]]></token>
101 <token name="@SCAN_INPUTS@"> 87 <token name="@SCAN_INPUTS@">
102 -i '$inputs_dir' 88 -i '$inputs_dir'
103 </token> 89 </token>
104 90
105 <xml name="fasta_input"> 91 <xml name="fasta_input">
106 <param argument="-f" type="data" format="fasta" label="Background protein fasta database"/> 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>
107 </xml> 95 </xml>
108 <token name="@LINK_FASTA_INPUT@"><![CDATA[ 96 <token name="@LINK_FASTA_INPUT@"><![CDATA[
109 #set $f_name = $ln_name($f) 97 #set $f_name = $ln_name($fasta)
110 ln -s '$f' '$f_name' && 98 ln -s '$fasta' '$f_name' &&
111 ]]></token> 99 ]]></token>
112 <token name="@FASTA_INPUT@"> 100 <token name="@FASTA_INPUT@">
113 -f '$f_name' 101 -f '$f_name'
114 </token> 102 </token>
115 103
116 <xml name="target_fasta"> 104 <xml name="target_fasta">
117 <param argument="-t" type="data" format="fasta" label="target FASTA file" optional="true"/> 105 <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true">
118 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/> 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>
119 </xml> 111 </xml>
120 <token name="@LINK_TARGET_FASTA@"><![CDATA[ 112 <token name="@LINK_TARGET_FASTA@"><![CDATA[
121 #if $t 113 #if $target_fasta
122 #set $t_name = $ln_name($t) 114 #set $t_name = $ln_name($target_fasta)
123 ln -s '$t' '$t_name' && 115 ln -s '$target_fasta' '$t_name' &&
124 #else 116 #else
125 #set $t_name = None 117 #set $t_name = None
126 #end if 118 #end if
127 ]]></token> 119 ]]></token>
128 <token name="@TARGET_FASTA@"> 120 <token name="@TARGET_FASTA@">
130 -t '$t_name' 122 -t '$t_name'
131 -tp $tp 123 -tp $tp
132 #end if 124 #end if
133 </token> 125 </token>
134 126
135 <xml name="lib_input" token_optional="true" token_help=""> 127 <xml name="lib_input" token_optional="true" token_libhelp="">
136 <param argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB"> 128 <param name="library" argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB">
137 <help>@HELP@</help> 129 <help>@LIBHELP@</help>
138 </param> 130 </param>
139 </xml> 131 </xml>
140 <token name="@LINK_LIB_INPUT@"><![CDATA[ 132 <token name="@LINK_LIB_INPUT@"><![CDATA[
141 #if $l 133 #if $library
142 #set $l_name = $ln_name($l) 134 #set $l_name = $ln_name($library)
143 cp '$l' $l_name && 135 cp '$library' '$l_name' &&
144 #else 136 #else
145 #set $l_name = None 137 #set $l_name = None
146 #end if 138 #end if
147 ]]></token> 139 ]]></token>
148 <token name="@LIB_INPUT@"> 140 <token name="@LIB_INPUT@">
193 <xml name="walnut_common_options"> 185 <xml name="walnut_common_options">
194 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true" 186 <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true"
195 token_cid_selected="false" token_hcd_selected="true"/> 187 token_cid_selected="false" token_hcd_selected="true"/>
196 </xml> 188 </xml>
197 <token name="@COMMON_OPTIONS@"> 189 <token name="@COMMON_OPTIONS@">
198 #if $acquisition.set_acquisition == 'yes' 190 #if $options.acquisition.set_acquisition == 'yes'
199 -numberOfExtraDecoyLibrariesSearched $acquisition.numberOfExtraDecoyLibrariesSearched 191 -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched
200 #if $acquisition.acquisition 192 #if $options.acquisition.acquisition
201 -acquisition '$acquisition.acquisition' 193 -acquisition '$options.acquisition.acquisition'
202 #end if 194 #end if
203 #if $acquisition.enzyme: 195 #if $options.acquisition.enzyme:
204 -enzyme '$acquisition.enzyme' 196 -enzyme '$options.acquisition.enzyme'
205 #end if 197 #end if
206 #if $acquisition.frag: 198 #if $options.acquisition.frag:
207 -frag '$acquisition.frag' 199 -frag '$options.acquisition.frag'
208 #end if 200 #end if
209 #end if 201 #end if
210 </token> 202 </token>
211 203
212 <xml name="mass_tolerance"> 204 <xml name="mass_tolerance">
252 <yield/> 244 <yield/>
253 </when> 245 </when>
254 </conditional> 246 </conditional>
255 </xml> 247 </xml>
256 <token name="@MASS_TOLERANCE@"> 248 <token name="@MASS_TOLERANCE@">
257 #if $tolerance.set_tolerance == 'yes' 249 #if $options.tolerance.set_tolerance == 'yes'
258 -ptolunits $tolerance.precursor_tolerance.ptolunits 250 -ptolunits $options.tolerance.precursor_tolerance.ptolunits
259 -ptol $tolerance.precursor_tolerance.ptol 251 -ptol $options.tolerance.precursor_tolerance.ptol
260 -ftolunits $tolerance.fragment_tolerance.ftolunits 252 -ftolunits $options.tolerance.fragment_tolerance.ftolunits
261 -ftol $tolerance.fragment_tolerance.ftol 253 -ftol $options.tolerance.fragment_tolerance.ftol
262 #end if 254 #end if
263 </token> 255 </token>
264 256
265 <xml name="mass_library_tolerance"> 257 <xml name="mass_library_tolerance">
266 <expand macro="mass_tolerance"> 258 <expand macro="mass_tolerance">
284 </conditional> 276 </conditional>
285 </expand> 277 </expand>
286 </xml> 278 </xml>
287 <token name="@MASS_LIBRARY_TOLERANCE@"> 279 <token name="@MASS_LIBRARY_TOLERANCE@">
288 @MASS_TOLERANCE@ 280 @MASS_TOLERANCE@
289 #if $tolerance.set_tolerance == 'yes' and $tolerance.library_tolerance.ltolunits != 'defaults' 281 #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults'
290 -ltolunits $tolerance.library_tolerance.ltolunits 282 -ltolunits $options.tolerance.library_tolerance.ltolunits
291 -ltol $tolerance.library_tolerance.ltol 283 -ltol $options.tolerance.library_tolerance.ltol
292 #end if 284 #end if
293 </token> 285 </token>
294 286
295 <xml name="percolator_options"> 287 <xml name="percolator_options">
296 <conditional name="percolator"> 288 <conditional name="percolator">
305 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/> 297 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
306 </when> 298 </when>
307 </conditional> 299 </conditional>
308 </xml> 300 </xml>
309 <token name="@PERCOLATOR_OPTIONS@"> 301 <token name="@PERCOLATOR_OPTIONS@">
310 #if $percolator.set_percolator == 'yes' 302 #if $options.percolator.set_percolator == 'yes'
311 #if str($percolator.percolatorVersionNumber) 303 #if str($options.percolator.percolatorVersionNumber)
312 -percolatorVersionNumber $percolator.percolatorVersionNumber 304 -percolatorVersionNumber $options.percolator.percolatorVersionNumber
313 #end if 305 #end if
314 #if str($percolator.percolatorProteinThreshold) 306 #if str($options.percolator.percolatorProteinThreshold)
315 -percolatorProteinThreshold $percolator.percolatorProteinThreshold 307 -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
316 #end if 308 #end if
317 #if str($percolator.percolatorThreshold) 309 #if str($options.percolator.percolatorThreshold)
318 -percolatorThreshold $percolator.percolatorThreshold 310 -percolatorThreshold $options.percolator.percolatorThreshold
319 #end if 311 #end if
320 #end if 312 #end if
321 </token> 313 </token>
322 314
323 <xml name="peak_options"> 315 <xml name="peak_options">
339 </param> 331 </param>
340 </when> 332 </when>
341 </conditional> 333 </conditional>
342 </xml> 334 </xml>
343 <token name="@PEAK_OPTIONS@"> 335 <token name="@PEAK_OPTIONS@">
344 #if $peak.set_peak == 'yes' 336 #if $options.peak.set_peak == 'yes'
345 #if str($peak.numberOfQuantitativePeaks) 337 #if str($options.peak.numberOfQuantitativePeaks)
346 -numberOfQuantitativePeaks $peak.numberOfQuantitativePeaks 338 -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks
347 #end if 339 #end if
348 #if str($peak.minNumOfQuantitativePeaks) 340 #if str($options.peak.minNumOfQuantitativePeaks)
349 -minNumOfQuantitativePeaks $peak.minNumOfQuantitativePeaks 341 -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks
350 #end if 342 #end if
351 #if str($peak.minQuantitativeIonNumber) 343 #if str($options.peak.minQuantitativeIonNumber)
352 -minQuantitativeIonNumber $peak.minQuantitativeIonNumber 344 -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber
353 #end if 345 #end if
354 #if str($peak.minIntensity) 346 #if str($options.peak.minIntensity)
355 -minIntensity $peak.minIntensity 347 -minIntensity $options.peak.minIntensity
356 #end if 348 #end if
357 #if str($peak.expectedPeakWidth) 349 #if str($options.peak.expectedPeakWidth)
358 -expectedPeakWidth $peak.expectedPeakWidth 350 -expectedPeakWidth $options.peak.expectedPeakWidth
359 #end if 351 #end if
360 #if $peak.filterPeaklists 352 #if $options.peak.filterPeaklists
361 -filterPeaklists $peak.filterPeaklists 353 -filterPeaklists $options.peak.filterPeaklists
362 #end if 354 #end if
363 #end if 355 #end if
364 </token> 356 </token>
365 357
366 <xml name="window_options"> 358 <xml name="window_options">
385 </param> 377 </param>
386 </when> 378 </when>
387 </conditional> 379 </conditional>
388 </xml> 380 </xml>
389 <token name="@WINDOW_OPTIONS@"> 381 <token name="@WINDOW_OPTIONS@">
390 #if $window.set_window == 'yes' 382 #if $options.window.set_window == 'yes'
391 #if str($window.foffset) 383 #if str($options.window.foffset)
392 -foffset $window.foffset 384 -foffset $options.window.foffset
393 #end if 385 #end if
394 #if str($window.poffset) 386 #if str($options.window.poffset)
395 -poffset $window.poffset 387 -poffset $options.window.poffset
396 #end if 388 #end if
397 #if str($window.precursorIsolationMargin) 389 #if str($options.window.precursorIsolationMargin)
398 -precursorIsolationMargin $window.precursorIsolationMargin 390 -precursorIsolationMargin $options.window.precursorIsolationMargin
399 #end if 391 #end if
400 #if str($window.precursorWindowSize) 392 #if str($options.window.precursorWindowSize)
401 -precursorWindowSize $window.precursorWindowSize 393 -precursorWindowSize $options.window.precursorWindowSize
402 #end if 394 #end if
403 #if str($window.rtWindowInMin) 395 #if str($options.window.rtWindowInMin)
404 -rtWindowInMin $window.rtWindowInMin 396 -rtWindowInMin $options.window.rtWindowInMin
405 #end if 397 #end if
406 #if $window.scoringBreadthType 398 #if $options.window.scoringBreadthType
407 -scoringBreadthType $window.scoringBreadthType 399 -scoringBreadthType $options.window.scoringBreadthType
408 #end if 400 #end if
409 #end if 401 #end if
410 </token> 402 </token>
411 403
412 <xml name="modification_options"> 404 <xml name="modification_options">
431 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/> 423 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/>
432 </when> 424 </when>
433 </conditional> 425 </conditional>
434 </xml> 426 </xml>
435 <token name="@MODIFICATION_OPTIONS@"> 427 <token name="@MODIFICATION_OPTIONS@">
436 #if $modifications.set_modifications == 'yes' 428 #if $options.modifications.set_modifications == 'yes'
437 #if $modifications.fixed 429 #if $options.modifications.fixed
438 -fixed $modifications.fixed 430 -fixed $options.modifications.fixed
439 #end if 431 #end if
440 -verifyModificationIons $modifications.verifyModificationIons 432 -verifyModificationIons $options.modifications.verifyModificationIons
441 #end if 433 #end if
442 </token> 434 </token>
443 435
444 <xml name="search_options"> 436 <xml name="search_options">
445 <conditional name="search"> 437 <conditional name="search">
457 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/> 449 <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"/> 450 <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"/> 451 <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"/> 452 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>
461 <!-- 453 <!--
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"/> 454 <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"/> 455 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>
466 --> 456 -->
467 </when> 457 </when>
468 </conditional> 458 </conditional>
469 </xml> 459 </xml>
470 <token name="@SEARCH_OPTIONS@"> 460 <token name="@SEARCH_OPTIONS@">
471 #if $search.set_search == 'yes' 461 #if $options.search.set_search == 'yes'
472 -minCharge $search.minCharge 462 -minCharge $options.search.minCharge
473 -maxCharge $search.maxCharge 463 -maxCharge $options.search.maxCharge
474 -minLength $search.minLength 464 -minLength $options.search.minLength
475 -maxLength $search.maxLength 465 -maxLength $options.search.maxLength
476 -minEluteTime $search.minEluteTime 466 -minEluteTime $options.search.minEluteTime
477 -maxMissedCleavage $search.maxMissedCleavage 467 -maxMissedCleavage $options.search.maxMissedCleavage
478 -minQuantitativeIonNumber $search.minQuantitativeIonNumber 468 -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber
479 -minNumOfQuantitativePeaks $search.minNumOfQuantitativePeaks 469 -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks
480 -numberOfQuantitativePeaks $search.numberOfQuantitativePeaks 470 -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks
481 ## -alpha $search.alpha 471 ## -addDecoysToBackground $options.search.addDecoysToBackground
482 ## -beta $search.beta 472 ## -dontRunDecoys $options.search.dontRunDecoys
483 ## -addDecoysToBackground $search.addDecoysToBackground 473 #end if
484 ## -dontRunDecoys $search.dontRunDecoys 474 </token>
485 #end if 475
486 </token> 476 <xml name="options_section">
487 <!-- 477 <section name="options" title="Parameter Settings" expanded="false">
488 minNumOfQuantitativePeaks minQuantitativeIonNumber numberOfQuantitativePeaks numberOfReportedPeaksu 478 <expand macro="common_options"/>
489 +acquisition (default: overlapping dia) 479 <expand macro="mass_library_tolerance"/>
490 +addDecoysToBackground (default: false) 480 <expand macro="percolator_options"/>
491 +alpha (default: 1.8) 481 <expand macro="peak_options"/>
492 +beta (default: 0.4) 482 <expand macro="window_options"/>
493 +dontRunDecoys (default: false) 483 <expand macro="modification_options"/>
494 +enzyme (default: trypsin) 484 <expand macro="search_options"/>
495 +filterPeaklists (default: false) 485 </section>
496 +fixed (default: C=57.0214635) 486 </xml>
497 +foffset (default: 0) 487
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"> 488 <xml name="libexport">
527 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/> 489 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/>
528 </xml> 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>
529 </macros> 551 </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 -->