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comparison macros.xml @ 0:e8d7b7dc55fc draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metamorpheus commit 7a40b99b4124b0c032a16067741fd55a60b48cb0-dirty"
author galaxyp
date Wed, 26 May 2021 15:42:20 +0000
parents
children 975f857ad9b8
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-1:000000000000 0:e8d7b7dc55fc
1 <macros>
2 <token name="@PROFILE@">21.01</token>
3 <token name="@TOOL_VERSION@">0.0.316</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">metamorpheus</requirement>
8 <yield/>
9 </requirements>
10 </xml>
11
12 <token name="@DEFAULT_COMMON_TOML@">
13 [CommonParameters]
14 # MaxThreadsToUsePerFile = 11
15 ListOfModsFixed = "Common Fixed\tCarbamidomethyl on C\t\tCommon Fixed\tCarbamidomethyl on U"
16 ListOfModsVariable = "Common Variable\tOxidation on M"
17 DoPrecursorDeconvolution = true # Calibration false
18 UseProvidedPrecursorInfo = true
19 DeconvolutionIntensityRatio = 3.0
20 DeconvolutionMaxAssumedChargeState = 12
21 DeconvolutionMassTolerance = "±4.0000 PPM"
22 TotalPartitions = 1
23 ProductMassTolerance = "±20.0000 PPM" # Calibration 25.0000
24 PrecursorMassTolerance = "±5.0000 PPM" # Calibration 15.0000
25 AddCompIons = false
26 ScoreCutoff = 5.0
27 ReportAllAmbiguity = true
28 NumberOfPeaksToKeepPerWindow = 200
29 MinimumAllowedIntensityRatioToBasePeak = 0.01
30 NormalizePeaksAccrossAllWindows = false
31 TrimMs1Peaks = false
32 TrimMsMsPeaks = true # Calibration false
33 UseDeltaScore = false
34 QValueOutputFilter = 1.0
35 CustomIons = []
36 AssumeOrphanPeaksAreZ1Fragments = true
37 MaxHeterozygousVariants = 4
38 MinVariantDepth = 1
39 DissociationType = "HCD"
40 SeparationType = "HPLC"
41 MS2ChildScanDissociationType = "Unknown"
42 MS3ChildScanDissociationType = "Unknown"
43 </token>
44
45 <token name="@DEFAULT_DIGESTION_TOML@">
46 [CommonParameters.DigestionParams]
47 MaxMissedCleavages = 2
48 InitiatorMethionineBehavior = "Variable"
49 MinPeptideLength = 7
50 MaxPeptideLength = 2147483647
51 MaxModificationIsoforms = 1024
52 MaxModsForPeptide = 2
53 Protease = "trypsin"
54 SearchModeType = "Full"
55 FragmentationTerminus = "Both"
56 SpecificProtease = "trypsin"
57 GeneratehUnlabeledProteinsForSilac = true
58 </token>
59
60 <token name="@DEFAULT_CALIBRATION_TOML@"><![CDATA[
61 TaskType = "Calibrate"
62
63 [CalibrationParameters]
64 WriteIntermediateFiles = false
65 WriteIndexedMzml = true
66 MinMS1IsotopicPeaksNeededForConfirmedIdentification = 3
67 MinMS2IsotopicPeaksNeededForConfirmedIdentification = 2
68 NumFragmentsNeededForEveryIdentification = 10
69
70 [CommonParameters]
71 MaxThreadsToUsePerFile = 11
72 ListOfModsFixed = "Common Fixed\tCarbamidomethyl on C\t\tCommon Fixed\tCarbamidomethyl on U"
73 ListOfModsVariable = "Common Variable\tOxidation on M"
74 DoPrecursorDeconvolution = false
75 UseProvidedPrecursorInfo = true
76 DeconvolutionIntensityRatio = 3.0
77 DeconvolutionMaxAssumedChargeState = 12
78 DeconvolutionMassTolerance = "±4.0000 PPM"
79 TotalPartitions = 1
80 ProductMassTolerance = "±25.0000 PPM"
81 PrecursorMassTolerance = "±15.0000 PPM"
82 AddCompIons = false
83 ScoreCutoff = 5.0
84 ReportAllAmbiguity = true
85 NumberOfPeaksToKeepPerWindow = 200
86 MinimumAllowedIntensityRatioToBasePeak = 0.01
87 NormalizePeaksAccrossAllWindows = false
88 TrimMs1Peaks = false
89 TrimMsMsPeaks = false
90 UseDeltaScore = false
91 QValueOutputFilter = 1.0
92 CustomIons = []
93 AssumeOrphanPeaksAreZ1Fragments = true
94 MaxHeterozygousVariants = 4
95 MinVariantDepth = 1
96 DissociationType = "HCD"
97 SeparationType = "HPLC"
98 MS2ChildScanDissociationType = "Unknown"
99 MS3ChildScanDissociationType = "Unknown"
100
101 @DEFAULT_DIGESTION_TOML@
102 ]]></token>
103
104 <token name="@DEFAULT_GPTMD_TOML@"><![CDATA[
105 TaskType = "Gptmd"
106
107 [GptmdParameters]
108 ListOfModsGptmd = "Common Biological\tAcetylation on K\t\tCommon Biological\tAcetylation on X\t\tCommon Biological\tADP-ribosylation on S\t\tCommon Artifact\tAmmonia loss on C\t\tCommon Artifact\tAmmonia loss on N\t\tCommon Biological\tButyrylation on K\t\tMetal\tCalcium on D\t\tMetal\tCalcium on E\t\tCommon Artifact\tCarbamyl on C\t\tCommon Artifact\tCarbamyl on K\t\tCommon Artifact\tCarbamyl on M\t\tCommon Artifact\tCarbamyl on R\t\tCommon Artifact\tCarbamyl on X\t\tCommon Biological\tCarboxylation on D\t\tCommon Biological\tCarboxylation on E\t\tCommon Biological\tCarboxylation on K\t\tCommon Biological\tCitrullination on R\t\tCommon Biological\tCrotonylation on K\t\tMetal\tCu[I] on D\t\tMetal\tCu[I] on E\t\tCommon Artifact\tDeamidation on N\t\tCommon Artifact\tDeamidation on Q\t\tCommon Biological\tDimethylation on K\t\tCommon Biological\tDimethylation on R\t\tMetal\tFe[II] on D\t\tMetal\tFe[II] on E\t\tMetal\tFe[III] on D\t\tMetal\tFe[III] on E\t\tCommon Biological\tFormylation on K\t\tCommon Biological\tGlu to PyroGlu on Q\t\tCommon Biological\tGlutarylation on K\t\tCommon Biological\tHexNAc on Nxs\t\tCommon Biological\tHexNAc on Nxt\t\tCommon Biological\tHexNAc on S\t\tCommon Biological\tHexNAc on T\t\tCommon Biological\tHydroxybutyrylation on K\t\tCommon Biological\tHydroxylation on K\t\tCommon Biological\tHydroxylation on N\t\tCommon Biological\tHydroxylation on P\t\tMetal\tMagnesium on D\t\tMetal\tMagnesium on E\t\tCommon Biological\tMalonylation on K\t\tCommon Biological\tMethylation on K\t\tCommon Biological\tMethylation on R\t\tCommon Biological\tNitrosylation on C\t\tCommon Biological\tNitrosylation on Y\t\tCommon Biological\tPhosphorylation on S\t\tCommon Biological\tPhosphorylation on T\t\tCommon Biological\tPhosphorylation on Y\t\tMetal\tPotassium on D\t\tMetal\tPotassium on E\t\tCommon Biological\tPyridoxal phosphate on K\t\tMetal\tSodium on D\t\tMetal\tSodium on E\t\tCommon Biological\tSuccinylation on K\t\tCommon Biological\tSulfonation on Y\t\tCommon Biological\tTrimethylation on K\t\tCommon Artifact\tWater Loss on E\t\tMetal\tZinc on D\t\tMetal\tZinc on E"
109
110 @DEFAULT_COMMON_TOML@
111
112 @DEFAULT_DIGESTION_TOML@
113 ]]></token>
114
115 <token name="@DEFAULT_SEARCH_TOML@"><![CDATA[
116 TaskType = "Search"
117
118 [SearchParameters]
119 DisposeOfFileWhenDone = true
120 DoParsimony = true
121 ModPeptidesAreDifferent = false
122 NoOneHitWonders = false
123 MatchBetweenRuns = false
124 Normalize = false
125 QuantifyPpmTol = 5.0
126 DoHistogramAnalysis = false
127 SearchTarget = true
128 DecoyType = "Reverse"
129 MassDiffAcceptorType = "OneMM"
130 WritePrunedDatabase = false
131 KeepAllUniprotMods = true
132 DoLocalizationAnalysis = true
133 DoQuantification = true
134 SearchType = "Classic"
135 LocalFdrCategories = ["FullySpecific"]
136 MaxFragmentSize = 30000.0
137 HistogramBinTolInDaltons = 0.003
138 MaximumMassThatFragmentIonScoreIsDoubled = 0.0
139 WriteMzId = true
140 WritePepXml = false
141 WriteDecoys = true
142 WriteContaminants = true
143 WriteIndividualFiles = true
144 CompressIndividualFiles = false
145 TCAmbiguity = "RemoveContaminant"
146
147 [SearchParameters.ModsToWriteSelection]
148 'N-linked glycosylation' = 3
149 'O-linked glycosylation' = 3
150 'Other glycosylation' = 3
151 'Common Biological' = 3
152 'Less Common' = 3
153 Metal = 3
154 '2+ nucleotide substitution' = 3
155 '1 nucleotide substitution' = 3
156 UniProt = 2
157
158 @DEFAULT_COMMON_TOML@
159
160 @DEFAULT_DIGESTION_TOML@
161 ]]></token>
162
163 <xml name="input_spectrums" token_multiple="false" token_filetype="Spectrum">
164 <param name="spectrums" type="data" format="mzml" multiple="@MULTIPLE@" label="MS/MS @FILETYPE@ files"/>
165 </xml>
166 <xml name="calib_toml">
167 <param name="calib_tomls" type="data" format="toml" multiple="true" optional="true" label="Calibrated Spectrum TOML files"/>
168 </xml>
169 <xml name="input_databases">
170 <param name="databases" type="data" format="uniprotxml,fasta" multiple="true" label="Reference Protein Databases"/>
171 </xml>
172 <xml name="input_toml">
173 <param name="input_toml" type="data" format="toml" optional="true" label="Optional Config toml from history"/>
174 </xml>
175 <token name="@CMD_IMPORTS@">
176 #import re
177 #def identifier_or_name($input1)
178 #if hasattr($input1, 'element_identifier')
179 #return $input1.element_identifier
180 #else
181 #return $input1.name
182 #end if
183 #end def
184 #def clean($name1)
185 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|xml|imzml|mzml|raw|mgf)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
186 #return $name_clean
187 #end def
188 #def ln_name($ds)
189 #set $ext = ''
190 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
191 #set $ext = ".mzML"
192 #else if $ds.is_of_type('thermo.raw')
193 #set $ext = ".raw"
194 #else if $ds.is_of_type('toml')
195 #set $ext = ".toml"
196 #else if $ds.is_of_type('uniprotxml')
197 #set $ext = ".xml"
198 #else if $ds.is_of_type('fasta')
199 #set $ext = ".fasta"
200 #end if
201 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
202 #return $name
203 #end def
204 </token>
205
206 <token name="@PREPARE_INPUTS@"><![CDATA[
207 @CMD_IMPORTS@
208 #set $spectrum_names = []
209 #set $database_names = []
210 #set $inputs_dir = 'inputs'
211 mkdir -p $inputs_dir &&
212 #for $sf in $spectrums
213 #set $i_name = $ln_name($sf)
214 $spectrum_names.append($i_name)
215 ln -s '${sf}' '${inputs_dir}/${i_name}' &&
216 #end for
217 #for $db in $databases
218 #set $d_name = $ln_name($db)
219 $database_names.append($d_name)
220 ln -s '${db}' '${d_name}' &&
221 #end for
222 ]]></token>
223 <token name="@LN_CALIB_TOML@"><![CDATA[
224 #for $tf in $calib_tomls
225 #set $t_name = $ln_name($tf)
226 ln -s '${tf}' '${inputs_dir}/${t_name}' &&
227 #end for
228 ]]></token>
229
230 <token name="@MERGE_TOMLS@"><![CDATA[
231 #def merge_tomls($tomls, $merged):
232 #import re
233 #set $config = dict()
234 #set $config['categories'] = []
235 #set $category = ' '
236 #for $toml in $tomls
237 #set $fh = open(toml,'r')
238 #for $line in $fh:
239 #set $entry = $line.rstrip()
240 #if $entry.strip() == '':
241 #continue
242 #end if
243 #set $m = $re.match('^((TaskType)\s*=\s*(.*))$', $entry)
244 #if $m:
245 #if $m.groups()[0] not in $config:
246 #set $config['TaskType'] = $entry
247 #continue
248 #end if
249 #end if
250 #set $m = $re.match('^(\[.+\])$', $entry)
251 #if $m:
252 #set $category = $m.groups()[0]
253 #if $category not in $config['categories']:
254 $config['categories'].append($category)
255 #set $config[$category] = []
256 #continue
257 #end if
258 #end if
259 #set $m = $re.match('^(\S+)\s*=\s*(.*)$',$entry)
260 #if $m:
261 #set $pname = $m.groups()[0]
262 #set $pval = $m.groups()[1]
263 #if $pname not in $config[$category]:
264 $config[$category].append($pname)
265 #end if
266 #set $config[$pname] = $pval
267 #end if
268 #*
269 *#
270 #end for
271 $fh.close()
272 #end for
273 #set $wfh = open($merged,'w')
274 #if 'TaskType' in $config:
275 #silent $wfh.write('%s\n' % $config['TaskType'])
276 #end if
277 #for $category in $config['categories']:
278 #silent $wfh.write('\n')
279 #silent $wfh.write('%s\n' % $category)
280 #for $pname in $config[$category]:
281 #set $pval = $config[$pname]
282 #silent $wfh.write('%s = %s\n' % ($pname, $pval))
283 #end for
284 #end for
285 $wfh.close()
286 #*
287 *#
288 #*
289 #echo $config
290 *#
291 #end def
292 #if $input_toml
293 $merge_tomls([$default_toml,str($input_toml),$user_toml], $task_settings_toml)
294 #else
295 $merge_tomls([$default_toml,$user_toml], $task_settings_toml)
296 #end if
297 ln -s '$task_settings_toml' tasksettings.toml &&
298
299 ]]></token>
300
301 <xml name="calibrate_params">
302 <conditional name="calibration">
303 <param name="set_calibration" type="select" label="Set Calibration Parameters">
304 <option value="no">no</option>
305 <option value="yes">yes</option>
306 </param>
307 <when value="no"/>
308 <when value="yes">
309 <param argument="MinMS1IsotopicPeaksNeededForConfirmedIdentification" type="integer" value="3" label="MinMS1IsotopicPeaksNeededForConfirmedIdentification"/>
310 <param argument="MinMS2IsotopicPeaksNeededForConfirmedIdentification" type="integer" value="2" label="MinMS2IsotopicPeaksNeededForConfirmedIdentification"/>
311 <param argument="NumFragmentsNeededForEveryIdentification" type="integer" value="10" label="NumFragmentsNeededForEveryIdentification"/>
312 </when>
313 </conditional>
314 </xml>
315 <token name="@CALIBRATE_CONFIG@"><![CDATA[
316 #if $calibration.set_calibration == 'yes'
317 [CalibrationParameters]
318 WriteIntermediateFiles = false
319 MinMS1IsotopicPeaksNeededForConfirmedIdentification = $calibration.MinMS1IsotopicPeaksNeededForConfirmedIdentification
320 MinMS2IsotopicPeaksNeededForConfirmedIdentification = $calibration.MinMS2IsotopicPeaksNeededForConfirmedIdentification
321 NumFragmentsNeededForEveryIdentification = $calibration.NumFragmentsNeededForEveryIdentification
322 #end if
323 ]]></token>
324 <xml name="gptmd_params">
325
326 </xml>
327 <token name="@GPTMD_CONFIG@">
328 TaskType = "Gptmd"
329
330 [GptmdParameters]
331 ListOfModsGptmd = "Common Biological\tAcetylation on K\t\tCommon Biological\tAcetylation on X\t\tCommon Biological\tADP-ribosylation on S\t\tCommon Biological\tButyrylation on K\t\tCommon Biological\tCarboxylation on D\t\tCommon Biological\tCarboxylation on E\t\tCommon Biological\tCarboxylation on K\t\tCommon Biological\tCitrullination on R\t\tCommon Biological\tCrotonylation on K\t\tCommon Biological\tDimethylation on K\t\tCommon Biological\tDimethylation on R\t\tCommon Biological\tFormylation on K\t\tCommon Biological\tGlu to PyroGlu on Q\t\tCommon Biological\tGlutarylation on K\t\tCommon Biological\tHexNAc on Nxs\t\tCommon Biological\tHexNAc on Nxt\t\tCommon Biological\tHexNAc on S\t\tCommon Biological\tHexNAc on T\t\tCommon Biological\tHydroxybutyrylation on K\t\tCommon Biological\tHydroxylation on K\t\tCommon Biological\tHydroxylation on N\t\tCommon Biological\tHydroxylation on P\t\tCommon Biological\tMalonylation on K\t\tCommon Biological\tMethylation on K\t\tCommon Biological\tMethylation on R\t\tCommon Biological\tNitrosylation on C\t\tCommon Biological\tNitrosylation on Y\t\tCommon Biological\tPhosphorylation on S\t\tCommon Biological\tPhosphorylation on T\t\tCommon Biological\tPhosphorylation on Y\t\tCommon Biological\tPyridoxal phosphate on K\t\tCommon Biological\tSuccinylation on K\t\tCommon Biological\tSulfonation on Y\t\tCommon Biological\tTrimethylation on K\t\tCommon Artifact\tAmmonia loss on C\t\tCommon Artifact\tAmmonia loss on N\t\tCommon Artifact\tCarbamyl on C\t\tCommon Artifact\tCarbamyl on K\t\tCommon Artifact\tCarbamyl on M\t\tCommon Artifact\tCarbamyl on R\t\tCommon Artifact\tCarbamyl on X\t\tCommon Artifact\tDeamidation on N\t\tCommon Artifact\tDeamidation on Q\t\tCommon Artifact\tWater Loss on E\t\tMetal\tCalcium on D\t\tMetal\tCalcium on E\t\tMetal\tCu[I] on D\t\tMetal\tCu[I] on E\t\tMetal\tFe[II] on D\t\tMetal\tFe[II] on E\t\tMetal\tFe[III] on D\t\tMetal\tFe[III] on E\t\tMetal\tMagnesium on D\t\tMetal\tMagnesium on E\t\tMetal\tPotassium on D\t\tMetal\tPotassium on E\t\tMetal\tSodium on D\t\tMetal\tSodium on E\t\tMetal\tZinc on D\t\tMetal\tZinc on E"
332 </token>
333
334 <xml name="search_params">
335 <conditional name="search_params">
336 <param name="set_search_params" type="select" label="Set Search Parameters">
337 <option value="no">no</option>
338 <option value="yes">yes</option>
339 </param>
340 <when value="no"/>
341 <when value="yes">
342 <param argument="DoParsimony" type="boolean" truevalue="true" falsevalue="false" checked="true" label="DoParsimony"/>
343 <param argument="ModPeptidesAreDifferent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="ModPeptidesAreDifferent"/>
344 <param argument="NoOneHitWonders" type="boolean" truevalue="true" falsevalue="false" checked="false" label="NoOneHitWonders"/>
345 <param argument="MatchBetweenRuns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="MatchBetweenRuns"/>
346 <param argument="Normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Normalize"/>
347 <param argument="QuantifyPpmTol" type="float" value="5.0" label="QuantifyPpmTol"/>
348 <param argument="DoHistogramAnalysis" type="boolean" truevalue="true" falsevalue="false" checked="false" label="DoHistogramAnalysis"/>
349 <param argument="SearchTarget" type="boolean" truevalue="true" falsevalue="false" checked="true" label="SearchTarget"/>
350 <param argument="DecoyType" type="select" label="DecoyType">
351 <option value="Reverse" selected="true">Reverse</option>
352 <option value="Slide">Slide</option>
353 <option value="None">None</option>
354 </param>
355 <param argument="MassDiffAcceptorType" type="select" label="MassDiffAcceptorType">
356 <option value="Exact">Exact</option>
357 <option value="OneMM" selected="true">OneMM</option>
358 <option value="TwoMM">TwoMM</option>
359 <option value="ThreeMM">ThreeMM</option>
360 <option value="PlusOrMinusThreeMM">PlusOrMinusThreeMM</option>
361 <option value="ModOpen">ModOpen</option>
362 <option value="Open">Open</option>
363 </param>
364 <param argument="KeepAllUniprotMods" type="boolean" truevalue="true" falsevalue="false" checked="true" label="KeepAllUniprotMods"/>
365 <param argument="DoLocalizationAnalysis" type="boolean" truevalue="true" falsevalue="false" checked="true" label="DoLocalizationAnalysis"/>
366 <param argument="DoQuantification" type="boolean" truevalue="true" falsevalue="false" checked="true" label="DoQuantification"/>
367 <param argument="SearchType" type="select" label="SearchType">
368 <option value="Classic" selected="true">Classic</option>
369 <option value="Modern">Modern</option>
370 <option value="NonSpecific">NonSpecific</option>
371 </param>
372 <param argument="LocalFdrCategories" type="select" label="LocalFdrCategories">
373 <option value="FullySpecific" selected="true">FullySpecific</option>
374 <option value="SemiSpecific">SemiSpecific</option>
375 <option value="NonSpecific">NonSpecific</option>
376 </param>
377 <param argument="MaxFragmentSize" type="float" value="30000.0" label="MaxFragmentSize"/>
378 <param argument="HistogramBinTolInDaltons" type="float" value="0.003" label="HistogramBinTolInDaltons"/>
379 <param argument="MaximumMassThatFragmentIonScoreIsDoubled" type="float" value="0.0" label="MaximumMassThatFragmentIonScoreIsDoubled"/>
380 </when>
381 </conditional>
382 <param name="search_outputs" type="select" multiple="true" label="Select Optional Search Outputs">
383 <option value="WriteMzId" selected="true">WriteMzId</option>
384 <option value="WritePepXml" selected="false">WritePepXml</option>
385 <option value="WritePrunedDatabase" selected="true">WritePrunedDatabase</option>
386 <option value="WriteDecoys" selected="false">WriteDecoys</option>
387 <option value="WriteContaminants" selected="false">WriteContaminants</option>
388 </param>
389 </xml>
390 <token name="@SEARCH_CONFIG@"><![CDATA[
391 [SearchParameters]
392 #if $search_params.set_search_params == 'yes'
393 DisposeOfFileWhenDone = true
394 DoParsimony = $search_params.DoParsimony
395 ModPeptidesAreDifferent = $search_params.ModPeptidesAreDifferent
396 NoOneHitWonders = $search_params.NoOneHitWonders
397 MatchBetweenRuns = $search_params.MatchBetweenRuns
398 Normalize = $search_params.Normalize
399 QuantifyPpmTol = $search_params.QuantifyPpmTol
400 DoHistogramAnalysis = $search_params.DoHistogramAnalysis
401 SearchTarget = $search_params.SearchTarget
402 DecoyType = "$search_params.DecoyType"
403 MassDiffAcceptorType = "$search_params.MassDiffAcceptorType"
404 KeepAllUniprotMods = $search_params.KeepAllUniprotMods
405 DoLocalizationAnalysis = $search_params.DoLocalizationAnalysis
406 DoQuantification = $search_params.DoQuantification
407 SearchType = "$search_params.SearchType"
408 LocalFdrCategories = ["$search_params.LocalFdrCategories"]
409 MaxFragmentSize = $search_params.MaxFragmentSize
410 HistogramBinTolInDaltons = $search_params.HistogramBinTolInDaltons
411 MaximumMassThatFragmentIonScoreIsDoubled = $search_params.MaximumMassThatFragmentIonScoreIsDoubled
412 #end if
413 WritePrunedDatabase = #echo str('WritePrunedDatabase' in $search_outputs).lower()
414 WriteMzId = #echo str('WriteMzId' in $search_outputs).lower()
415 WritePepXml = #echo str('WritePepXml' in $search_outputs).lower()
416 WritePepXml = #echo str('WritePepXml' in $search_outputs).lower()
417 WriteDecoys = #echo str('WriteDecoys' in $search_outputs).lower()
418 WriteContaminants = #echo str('WriteContaminants' in $search_outputs).lower()
419
420 [SearchParameters.ModsToWriteSelection]
421 'N-linked glycosylation' = 3
422 'O-linked glycosylation' = 3
423 'Other glycosylation' = 3
424 'Common Biological' = 3
425 'Less Common' = 3
426 Metal = 3
427 '2+ nucleotide substitution' = 3
428 '1 nucleotide substitution' = 3
429 UniProt = 2
430 ]]></token>
431
432 <xml name="dissociation_options">
433 <option value="Any">Any</option>
434 <option value="CID">CID</option>
435 <option value="LowCID">LowCID</option>
436 <option value="ISCID">ISCID</option>
437 <option value="MPD">MPD</option>
438 <option value="ECD">ECD</option>
439 <option value="PQD">PQD</option>
440 <option value="ETD">ETD</option>
441 <option value="HCD" selected="true">HCD</option>
442 <option value="EThcD">EThcD</option>
443 <option value="Custom">Custom</option>
444 </xml>
445
446 <xml name="common_params">
447 <conditional name="common">
448 <param name="set_common" type="select" label="Set Common Parameters">
449 <option value="no">no</option>
450 <option value="yes">yes</option>
451 </param>
452 <when value="no"/>
453 <when value="yes">
454 <param argument="UseProvidedPrecursorInfo" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Provided Precursor"/>
455 <param argument="DoPrecursorDeconvolution" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Deconvolute Precursor"/>
456 <param argument="DeconvolutionMaxAssumedChargeState" type="integer" value="12" label="Deconvolution Max Assumed Charge State"/>
457 <param argument="DeconvolutionIntensityRatio" type="float" value="3.0" label="DeconvolutionIntensityRatio"/>
458 <param argument="DeconvolutionMassTolerance" type="float" value="4.0000" label="DeconvolutionMassTolerance in PPM"/>
459 <param argument="TotalPartitions" type="integer" value="1" label="TotalPartitions"/>
460 <param argument="PrecursorMassTolerance" type="float" value="15.0000" label="PrecursorMassTolerance in PPM"/>
461 <param argument="ProductMassTolerance" type="float" value="25.0000" label="ProductMassTolerance in PPM"/>
462 <param argument="AddCompIons" type="boolean" truevalue="true" falsevalue="false" checked="false" label="AddCompIons"/>
463 <param argument="ScoreCutoff" type="float" value="5.0" label="ScoreCutoff"/>
464 <param argument="ReportAllAmbiguity" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ReportAllAmbiguity"/>
465 <param argument="NumberOfPeaksToKeepPerWindow" type="integer" value="200" label="NumberOfPeaksToKeepPerWindow"/>
466 <param argument="MinimumAllowedIntensityRatioToBasePeak" type="float" value="0.01" label="MinimumAllowedIntensityRatioToBasePeak"/>
467 <param argument="NormalizePeaksAccrossAllWindows" type="boolean" truevalue="true" falsevalue="false" checked="false" label="NormalizePeaksAccrossAllWindows"/>
468 <param argument="TrimMs1Peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="TrimMs1Peaks"/>
469 <param argument="TrimMsMsPeaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="TrimMsMsPeaks"/>
470 <param argument="UseDeltaScore" type="boolean" truevalue="true" falsevalue="false" checked="false" label="UseDeltaScore"/>
471 <param argument="QValueOutputFilter" type="float" value="1.0" label="QValueOutputFilter"/>
472 <param argument="MaxHeterozygousVariants" type="integer" value="4" label="MaxHeterozygousVariants"/>
473 <param argument="MinVariantDepth" type="integer" value="1" label="MinVariantDepth"/>
474 <param argument="SeparationType" type="select" label="SeparationType">
475 <option value="HPLC" selected="true">HPLC</option>
476 <option value="CZE">CZE</option>
477 </param>
478 <param argument="DissociationType" type="select" label="DissociationType">
479 <expand macro="dissociation_options"/>
480 </param>
481 <param argument="MS2ChildScanDissociationType" type="select" label="MS2ChildScanDissociationType">
482 <expand macro="dissociation_options"/>
483 </param>
484 <param argument="MS3ChildScanDissociationType" type="select" label="MS2ChildScanDissociationType">
485 <expand macro="dissociation_options"/>
486 </param>
487 </when>
488 </conditional>
489 </xml>
490 <token name="@COMMON_CONFIG@">
491 [CommonParameters]
492 TaskDescriptor = "CalibrateTask"
493 MaxThreadsToUsePerFile = 11
494 #if $common.set_common == 'yes'
495 DoPrecursorDeconvolution = $common.DoPrecursorDeconvolution
496 UseProvidedPrecursorInfo = $common.UseProvidedPrecursorInfo
497 DeconvolutionIntensityRatio = $common.DeconvolutionIntensityRatio
498 DeconvolutionMaxAssumedChargeState = $common.DeconvolutionMaxAssumedChargeState
499 DeconvolutionMassTolerance = "±${common.DeconvolutionMassTolerance} PPM"
500 TotalPartitions = $common.TotalPartitions
501 ProductMassTolerance = "±${common.ProductMassTolerance} PPM"
502 PrecursorMassTolerance = "±${common.PrecursorMassTolerance} PPM"
503 AddCompIons = $common.AddCompIons
504 ScoreCutoff = $common.ScoreCutoff
505 ReportAllAmbiguity = $common.ReportAllAmbiguity
506 NumberOfPeaksToKeepPerWindow = $common.NumberOfPeaksToKeepPerWindow
507 MinimumAllowedIntensityRatioToBasePeak = $common.MinimumAllowedIntensityRatioToBasePeak
508 NormalizePeaksAccrossAllWindows = $common.NormalizePeaksAccrossAllWindows
509 TrimMs1Peaks = $common.TrimMs1Peaks
510 TrimMsMsPeaks = $common.TrimMsMsPeaks
511 UseDeltaScore = $common.UseDeltaScore
512 QValueOutputFilter = $common.QValueOutputFilter
513 ## CustomIons = $common.CustomIons
514 AssumeOrphanPeaksAreZ1Fragments = $common.AssumeOrphanPeaksAreZ1Fragments
515 MaxHeterozygousVariants = $common.MaxHeterozygousVariants
516 MinVariantDepth = $common.MinVariantDepth
517 DissociationType = $common.DissociationType
518 SeparationType = $common.SeparationType
519 MS2ChildScanDissociationType = $common.MS2ChildScanDissociationType
520 MS3ChildScanDissociationType = $common.MS3ChildScanDissociationType
521 #else
522 DoPrecursorDeconvolution = true
523 UseProvidedPrecursorInfo = true
524 DeconvolutionIntensityRatio = 3.0
525 DeconvolutionMaxAssumedChargeState = 12
526 DeconvolutionMassTolerance = "±4.0000 PPM"
527 TotalPartitions = 1
528 ProductMassTolerance = "±25.0000 PPM"
529 PrecursorMassTolerance = "±15.0000 PPM"
530 AddCompIons = false
531 ScoreCutoff = 5.0
532 ReportAllAmbiguity = true
533 NumberOfPeaksToKeepPerWindow = 200
534 MinimumAllowedIntensityRatioToBasePeak = 0.01
535 NormalizePeaksAccrossAllWindows = false
536 TrimMs1Peaks = false
537 TrimMsMsPeaks = true
538 UseDeltaScore = false
539 QValueOutputFilter = 1.0
540 CustomIons = []
541 AssumeOrphanPeaksAreZ1Fragments = true
542 MaxHeterozygousVariants = 4
543 MinVariantDepth = 1
544 DissociationType = "HCD"
545 SeparationType = "HPLC"
546 MS2ChildScanDissociationType = "Unknown"
547 MS3ChildScanDissociationType = "Unknown"
548 #end if
549 </token>
550 <xml name="mods_params">
551 </xml>
552 <token name="@MODS_CONFIG@">
553 ListOfModsFixed = "Common Fixed\tCarbamidomethyl on C\t\tCommon Fixed\tCarbamidomethyl on U"
554 ListOfModsVariable = "Common Variable\tOxidation on M"
555 </token>
556 <xml name="digest_params">
557 <conditional name="digest">
558 <param name="set_digest" type="select" label="Set Digest Parameters">
559 <option value="no">no</option>
560 <option value="yes">yes</option>
561 </param>
562 <when value="no"/>
563 <when value="yes">
564 <param name="Protease" type="select" label="Protease">
565 <option value="Any">Any</option>
566 <option value="Arg-C">Arg-C</option>
567 <option value="Asp-N">Asp-N</option>
568 <option value="chymotrypsin (don't cleave before proline)">chymotrypsin (don't cleave before proline)</option>
569 <option value="chymotrypsin (cleave before proline)">chymotrypsin (cleave before proline)</option>
570 <option value="CNBr">CNBr</option>
571 <option value="Glu-C">Glu-C</option>
572 <option value="Glu-C (with asp)">Glu-C (with asp)</option>
573 <option value="Lys-C (don't cleave before proline)">Lys-C (don't cleave before proline)</option>
574 <option value="Lys-C (cleave before proline)">Lys-C (cleave before proline)</option>
575 <option value="Lys-N">Lys-N</option>
576 <option value="semi-trypsin">semi-trypsin</option>
577 <option value="trypsin" selected="true">trypsin</option>
578 <option value="tryptophan oxidation">tryptophan oxidation</option>
579 <option value="non-specific">non-specific</option>
580 <option value="top-down">top-down</option>
581 <option value="singleN">singleN</option>
582 <option value="singleC">singleC</option>
583 <option value="collagenase">collagenase</option>
584 </param>
585 <param name="SpecificProtease" type="select" label="SpecificProtease">
586 <option value="Any">Any</option>
587 <option value="Arg-C">Arg-C</option>
588 <option value="Asp-N">Asp-N</option>
589 <option value="chymotrypsin (don't cleave before proline)">chymotrypsin (don't cleave before proline)</option>
590 <option value="chymotrypsin (cleave before proline)">chymotrypsin (cleave before proline)</option>
591 <option value="CNBr">CNBr</option>
592 <option value="Glu-C">Glu-C</option>
593 <option value="Glu-C (with asp)">Glu-C (with asp)</option>
594 <option value="Lys-C (don't cleave before proline)">Lys-C (don't cleave before proline)</option>
595 <option value="Lys-C (cleave before proline)">Lys-C (cleave before proline)</option>
596 <option value="Lys-N">Lys-N</option>
597 <option value="semi-trypsin">semi-trypsin</option>
598 <option value="trypsin" selected="true">trypsin</option>
599 <option value="tryptophan oxidation">tryptophan oxidation</option>
600 <option value="non-specific">non-specific</option>
601 <option value="top-down">top-down</option>
602 <option value="singleN">singleN</option>
603 <option value="singleC">singleC</option>
604 <option value="collagenase">collagenase</option>
605 </param>
606 <param name="InitiatorMethionineBehavior" type="select" label="InitiatorMethionineBehavior">
607 <option value="Variable" selected="true">Variable</option>
608 <option value="Undefined">Undefined</option>
609 <option value="Retain">Retain</option>
610 <option value="Cleave">Cleave</option>
611 </param>
612 <param name="SearchModeType" type="select" label="SearchModeType">
613 <option value="Full" selected="true">Full</option>
614 <option value="None">None</option>
615 <option value="Semi">Semi</option>
616 <option value="SingleN">SingleN</option>
617 <option value="SingleC">SingleC</option>
618 </param>
619 <param name="FragmentationTerminus" type="select" label="FragmentationTerminus">
620 <option value="Both" selected="true">Both</option>
621 <option value="None">None</option>
622 <option value="N">N</option>
623 <option value="C">C</option>
624 </param>
625 <param name="MaxMissedCleavages" type="integer" value="2" min="0" max="5" label="MaxMissedCleavages"/>
626 <param name="MinPeptideLength" type="integer" value="7" min="4" label="MinPeptideLength"/>
627 <param name="MaxPeptideLength" type="integer" value="2147483647" max="2147483647" label="MaxPeptideLength"/>
628 <param name="MaxModificationIsoforms" type="integer" value="1024" min="0" max="5000" label="MaxModificationIsoforms"/>
629 <param name="MaxModsForPeptide" type="integer" value="2" min="0" max="10" label="MaxModsForPeptide"/>
630 <param name="GeneratehUnlabeledProteinsForSilac" type="boolean" truevalue="true" falsevalue="false" checked="false" label="GeneratehUnlabeledProteinsForSilac"/>
631 </when>
632 </conditional>
633 </xml>
634 <token name="@DIGEST_CONFIG@">
635 [CommonParameters.DigestionParams]
636 #if $digest.set_digest == 'yes'
637 MaxMissedCleavages = $digest.MaxMissedCleavages
638 InitiatorMethionineBehavior = "$digest.InitiatorMethionineBehavior"
639 MinPeptideLength = $digest.MinPeptideLength
640 MaxPeptideLength = $digest.MaxPeptideLength
641 MaxModificationIsoforms = $digest.MaxModificationIsoforms
642 MaxModsForPeptide = $digest.MaxModsForPeptide
643 Protease = "$digest.Protease"
644 SearchModeType = "$digest.SearchModeType"
645 FragmentationTerminus = "$digest.FragmentationTerminus"
646 SpecificProtease = "$digest.SpecificProtease"
647 GeneratehUnlabeledProteinsForSilac = $digest.GeneratehUnlabeledProteinsForSilac
648 #else
649 MaxMissedCleavages = 2
650 InitiatorMethionineBehavior = "Variable"
651 MinPeptideLength = 7
652 MaxPeptideLength = 2147483647
653 MaxModificationIsoforms = 1024
654 MaxModsForPeptide = 2
655 Protease = "trypsin"
656 SearchModeType = "Full"
657 FragmentationTerminus = "Both"
658 SpecificProtease = "trypsin"
659 GeneratehUnlabeledProteinsForSilac = false
660 #end if
661 </token>
662
663
664 <xml name="output_settings_toml">
665 <data name="settings_toml" format="toml" label="${tool.name} on ${on_string} tasksettings.toml" from_work_dir="tasksettings.toml" />
666 </xml>
667 <xml name="calibrated_outputs">
668 <collection name="calibrated_scans" type="list" label="${tool.name} on ${on_string} Calibrated Spectrums">
669 <discover_datasets pattern="^(?P&lt;name&gt;.+\.mzML)$" ext="mzml" directory="output/Task1CalibrationTask" />
670 </collection>
671 <collection name="calibratation_toml" type="list" label="${tool.name} on ${on_string} Calibration TOMLs">
672 <discover_datasets pattern="^(?P&lt;name&gt;.+\.toml)$" ext="toml" directory="output/Task1CalibrationTask" />
673 </collection>
674 </xml>
675 <xml name="search_collection_outputs">
676 <collection name="mzids" type="list" label="${tool.name} on ${on_string} Spectrum Search mzIdent">
677 <filter>search_outputs and 'WriteMzId' in search_outputs</filter>
678 <discover_datasets pattern="^(?P&lt;name&gt;.+\.mzID)$" ext="mzid" directory="output/Task1SearchTask/Individual File Results" />
679 </collection>
680 <collection name="pepxmls" type="list" label="${tool.name} on ${on_string} Spectrum Search pep.xml">
681 <filter>search_outputs and 'WritePepXml' in search_outputs</filter>
682 <discover_datasets pattern="^(?P&lt;name&gt;.+\.pep\.XML)$" ext="pepxml" directory="output/Task1SearchTask/Individual File Results" />
683 </collection>
684 </xml>
685
686 <token name="@METAMORPHEUS_HELP@"><![CDATA[
687 **MetaMorpheus**
688
689 MetaMorpheus_ is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability.
690 See the wiki page for details: https://github.com/smith-chem-wisc/MetaMorpheus/wiki
691
692 Typical MetaMorpheus Workflow:
693
694 1. MetaMorpheus Calibration - of MassSpec Spectrum files using a reference protein database (preferably in Uniprot XML format)
695 2. MetaMorpheus G-PTM-D - Post-translational modification (PTM) discovery from the Calibrated Spectrum files
696 3. MetaMorpheus Database Search - Proetomics Search using the Calibrated Spectrum files and the GPTMD protein database
697
698 .. image:: MetaMorpheusWorkflow.png
699 :width: 823
700 :height: 759
701
702 .. _MetaMorpheus: https://github.com/smith-chem-wisc/MetaMorpheus
703
704 ]]></token>
705
706 <xml name="citations">
707 <citations>
708 <citation type="doi">10.1021/acs.jproteome.7b00873</citation>
709 <yield />
710 </citations>
711 </xml>
712
713 </macros>