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comparison macros.xml @ 0:39618cb4669f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
author galaxyp
date Fri, 20 Sep 2019 09:16:44 -0400
parents
children 8f2555d3687f
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-1:000000000000 0:39618cb4669f
1 <macros>
2 <token name="@VERSION@">0.9.0</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@VERSION@">encyclopedia</requirement>
6 <yield/>
7 </requirements>
8 </xml>
9 <xml name="citations">
10 <citations>
11 <yield />
12 </citations>
13 </xml>
14 <token name="@CMD_IMPORTS@">
15 #import re
16 #set $i_name = None
17 #set $f_name = None
18 #set $l_name = None
19 #set $t_name = None
20 </token>
21
22 <xml name="scan_input">
23 <param argument="-i" type="data" format="mzml" label="Spectrum file, .mzml or .dia"/>
24 </xml>
25 <token name="@LINK_SCAN_INPUT@"><![CDATA[
26 #set $i_name = $i.display_name
27 ln -s '$i' '$i_name' &&
28 ]]></token>
29 <token name="@SCAN_INPUT@">
30 -i '$i_name'
31 </token>
32
33 <xml name="scan_inputs">
34 <param argument="-i" type="data" format="mzml" multiple="true" label="Spectrum file, .mzml or .dia"/>
35 </xml>
36 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
37 #set $inputs_dir = 'inputs'
38 mkdir -p $inputs_dir &&
39 #for $sf in $i
40 #set $i_name = $sf.display_name
41 ln -s '$sf' '${inputs_dir}/${i_name}' &&
42 #end for
43 ]]></token>
44 <token name="@SCAN_INPUTS@">
45 -i '$inputs_dir'
46 </token>
47
48 <xml name="fasta_input">
49 <param argument="-f" type="data" format="fasta" label="Background protein fasta database"/>
50 </xml>
51 <token name="@LINK_FASTA_INPUT@"><![CDATA[
52 #set $f_name = $f.display_name
53 ln -s '$f' '$f_name' &&
54 ]]></token>
55 <token name="@FASTA_INPUT@">
56 -f '$f_name'
57 </token>
58
59 <xml name="target_fasta">
60 <param argument="-t" type="data" format="fasta" label="target FASTA file" optional="true"/>
61 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/>
62 </xml>
63 <token name="@LINK_TARGET_FASTA@"><![CDATA[
64 #if $t
65 #set $t_name = $t.display_name
66 ln -s '$t' '$t_name' &&
67 #else
68 #set $t_name = None
69 #end if
70 ]]></token>
71 <token name="@TARGET_FASTA@">
72 #if $t_name
73 -t '$t_name'
74 -tp $tp
75 #end if
76 </token>
77
78 <xml name="lib_input">
79 <param argument="-l" type="data" format="elib,dlib" label="Library: Chromatagram .ELIB or Spectrum .DLIB"/>
80 </xml>
81 <token name="@LINK_LIB_INPUT@"><![CDATA[
82 #set $l_name = $l.display_name
83 cp '$l' $l_name &&
84 ]]></token>
85 <token name="@LIB_INPUT@">
86 -l '$l_name'
87 </token>
88
89 <xml name="common_options">
90 <section name="acquisition" expanded="true" title="Acquisition Options">
91 <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/>
92 <param argument="-acquisition" type="select" label="Data Acquization Type">
93 <option value="Non-Overlapping DIA">Non-Overlapping DIA</option>
94 <option value="Overlapping DIA">Overlapping DIA</option>
95 </param>
96 <param argument="-enzyme" type="select" label="Digestion Enzyme">
97 <option value="Trypsin">Trypsin</option>
98 <option value="Trypsin/p">Trypsin/p</option>
99 <option value="Lys-C">Lys-C</option>
100 <option value="Lys-N">Lys-N</option>
101 <option value="Arg-C">Arg-C</option>
102 <option value="Glu-C">Glu-C</option>
103 <option value="Chymotrypsin">Chymotrypsin</option>
104 <option value="Pepsin A">Pepsin A</option>
105 <option value="Elastase">Elastase</option>
106 <option value="Thermolysin">Thermolysin</option>
107 <option value="No Enzyme">No Enzyme</option>
108 </param>
109 <param argument="-frag" type="select" label="Fragmentation">
110 <option value="CID">CID/HCD (B/Y)</option>
111 <option value="HCD">HCD (Y-Only)</option>
112 <option value="ETD">ETD (C/Z/Z+1)</option>
113 </param>
114 </section>
115 </xml>
116 <token name="@COMMON_OPTIONS@">
117 -numberOfExtraDecoyLibrariesSearched $acquisition.numberOfExtraDecoyLibrariesSearched
118 -acquisition '$acquisition.acquisition'
119 -enzyme '$acquisition.enzyme'
120 -frag '$acquisition.frag'
121 </token>
122
123 <xml name="mass_tolerance">
124 <section name="tolerance" expanded="true" title="Tolerance Options">
125 <conditional name="precursor_tolerance">
126 <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance">
127 <option value="PPM">PPM</option>
128 <option value="AMU">AMU</option>
129 <option value="Resolution">Resolution</option>
130 </param>
131 <when value="PPM">
132 <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/>
133 </when>
134 <when value="AMU">
135 <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/>
136 </when>
137 <when value="Resolution">
138 <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/>
139 </when>
140 </conditional>
141 <conditional name="fragment_tolerance">
142 <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance">
143 <option value="PPM">PPM</option>
144 <option value="AMU">AMU</option>
145 <option value="Resolution">Resolution</option>
146 </param>
147 <when value="PPM">
148 <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/>
149 </when>
150 <when value="AMU">
151 <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/>
152 </when>
153 <when value="Resolution">
154 <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/>
155 </when>
156 </conditional>
157 <yield/>
158 </section>
159 </xml>
160 <token name="@MASS_TOLERANCE@">
161 -ptolunits $tolerance.precursor_tolerance.ptolunits
162 -ptol $tolerance.precursor_tolerance.ptol
163 -ftolunits $tolerance.fragment_tolerance.ftolunits
164 -ftol $tolerance.fragment_tolerance.ftol
165 </token>
166
167 <xml name="mass_library_tolerance">
168 <expand macro="mass_tolerance">
169 <conditional name="library_tolerance">
170 <param argument="-ltolunits" type="select" label="Library Mass Tolerance">
171 <option value="PPM">PPM</option>
172 <option value="AMU">AMU</option>
173 <option value="Resolution">Resolution</option>
174 </param>
175 <when value="PPM">
176 <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/>
177 </when>
178 <when value="AMU">
179 <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/>
180 </when>
181 <when value="Resolution">
182 <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/>
183 </when>
184 </conditional>
185 </expand>
186 </xml>
187 <token name="@MASS_LIBRARY_TOLERANCE@">
188 @MASS_TOLERANCE@
189 -ltolunits $tolerance.library_tolerance.ltolunits
190 -ltol $tolerance.library_tolerance.ltol
191 </token>
192
193 <xml name="percolator_options">
194 <section name="percolator" expanded="false" title="Pecolator Options">
195 <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
196 <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
197 <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
198 </section>
199 </xml>
200 <token name="@PERCOLATOR_OPTIONS@">
201 #if str($percolator.percolatorVersionNumber)
202 -percolatorVersionNumber $percolator.percolatorVersionNumber
203 #end if
204 #if str($percolator.percolatorProteinThreshold)
205 -percolatorProteinThreshold $percolator.percolatorProteinThreshold
206 #end if
207 #if str($percolator.percolatorThreshold)
208 -percolatorThreshold $percolator.percolatorThreshold
209 #end if
210 </token>
211
212 <xml name="peak_options">
213 <section name="peak" expanded="false" title="Peak Options">
214 <param argument="-numberOfQuantitativePeaks" type="integer" value="5" min="1" max="100" label="Number of Quantitative Peaks"/>
215 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="0" max="100" label="Minimum Number of Quantitative Peaks"/>
216 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="0" max="100" label="Minimum Number of Quantitative Ions"/>
217 <param argument="-minIntensity" type="float" value="-1.0" label="minIntensity"/>
218 <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" label="Expected Peak Width"/>
219 <param argument="-filterPeaklists" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Filter Peak Lists"/>
220 </section>
221 </xml>
222 <token name="@PEAK_OPTIONS@">
223 #if str($peak.numberOfQuantitativePeaks)
224 -numberOfQuantitativePeaks $peak.numberOfQuantitativePeaks
225 #end if
226 #if str($peak.minNumOfQuantitativePeaks)
227 -minNumOfQuantitativePeaks $peak.minNumOfQuantitativePeaks
228 #end if
229 #if str($peak.minQuantitativeIonNumber)
230 -minQuantitativeIonNumber $peak.minQuantitativeIonNumber
231 #end if
232 #if str($peak.minIntensity)
233 -minIntensity $peak.minIntensity
234 #end if
235 #if str($peak.expectedPeakWidth)
236 -expectedPeakWidth $peak.expectedPeakWidth
237 #end if
238 -filterPeaklists $peak.filterPeaklists
239 </token>
240
241 <xml name="window_options">
242 <section name="window" expanded="false" title="Window Options">
243 <param argument="-foffset" type="integer" value="0" label="fragmentOffsetPPM"/>
244 <param argument="-poffset" type="integer" value="0" label="Precursor Offset PPM" help="-poffset"/>
245 <param argument="-precursorIsolationMargin" type="integer" value="0" label="precursorIsolationMargin"/>
246 <param argument="-precursorWindowSize" type="integer" value="-1" label="precursorWindowSize"/>
247 <param argument="-rtWindowInMin" type="float" value="-1.0" label="rtWindowInMin"/>
248 <param argument="-scoringBreadthType" type="select" label="scoringBreadthType">
249 <option value="window">Across entire window</option>
250 <option value="recal20">Recalibrated (20% gradient)</option>
251 <option value="recal">Recalibrated (peak width only)</option>
252 <option value="uncal20">Uncalibrated (20% gradient)</option>
253 <option value="uncal">Uncalibrated (peak width only)</option>
254 </param>
255 </section>
256 </xml>
257 <token name="@WINDOW_OPTIONS@">
258 -foffset $window.foffset
259 -poffset $window.poffset
260 -precursorIsolationMargin $window.precursorIsolationMargin
261 -precursorWindowSize $window.precursorWindowSize
262 -rtWindowInMin $window.rtWindowInMin
263 -scoringBreadthType $window.scoringBreadthType
264 </token>
265
266 <xml name="modification_options">
267 <section name="modifications" expanded="false" title="Modification Options">
268 <param argument="-fixed" type="select" label="Fixed Modification">
269 <option value="C=57.0214635">C=57.0214635</option>
270 </param>
271 <!--
272 <param argument="-localizationModification" type="select" optional="true" label="localizationModification">
273 </param>
274 -->
275 <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/>
276 </section>
277 </xml>
278 <token name="@MODIFICATION_OPTIONS@">
279 -verifyModificationIons $modifications.verifyModificationIons
280 </token>
281
282 <xml name="search_options">
283 <section name="search" expanded="false" title="Search Options">
284 <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/>
285 <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/>
286 <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/>
287 <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/>
288 <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/>
289 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/>
290 <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/>
291 <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/>
292 <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>
293 <param argument="-alpha" type="float" value="1.8" min="0.0" max="5.0" label="alpha"/>
294 <param argument="-beta" type="float" value="0.4" min="0.0" max="5.0" label="beta"/>
295 <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/>
296 <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>
297 </section>
298 </xml>
299 <token name="@SEARCH_OPTIONS@">
300 -minCharge $search.minCharge
301 -maxCharge $search.maxCharge
302 -minLength $search.minLength
303 -maxLength $search.maxLength
304 -minEluteTime $search.minEluteTime
305 -maxMissedCleavage $search.maxMissedCleavage
306 -minQuantitativeIonNumber $search.minQuantitativeIonNumber
307 -minNumOfQuantitativePeaks $search.minNumOfQuantitativePeaks
308 -numberOfQuantitativePeaks $search.numberOfQuantitativePeaks
309 -alpha $search.alpha
310 -beta $search.beta
311 -addDecoysToBackground $search.addDecoysToBackground
312 -dontRunDecoys $search.dontRunDecoys
313 </token>
314 minNumOfQuantitativePeaks minQuantitativeIonNumber numberOfQuantitativePeaks numberOfReportedPeaksu
315 <!--
316 +acquisition (default: overlapping dia)
317 +addDecoysToBackground (default: false)
318 +alpha (default: 1.8)
319 +beta (default: 0.4)
320 +dontRunDecoys (default: false)
321 +enzyme (default: trypsin)
322 +filterPeaklists (default: false)
323 +fixed (default: C=57.0214635)
324 +foffset (default: 0)
325 =frag (default: YONLY)
326 +ftol (default: 10)
327 +ftolunits (default: ppm)
328 +maxCharge (default: 3)
329 +maxLength (default: 100)
330 +maxMissedCleavage (default: 1)
331 +minCharge (default: 2)
332 +minEluteTime (default: 12)
333 +minIntensity (default: -1.0)
334 +minLength (default: 5)
335 +minNumOfQuantitativePeaks (default: 3)
336 +minQuantitativeIonNumber (default: 3)
337 +numberOfQuantitativePeaks (default: 5)
338 -numberOfReportedPeaks (default: 1)
339 -numberOfThreadsUsed (default: 12)
340 +percolatorProteinThreshol (default: 0.01)
341 +percolatorThreshold (default: 0.01)
342 +percolatorVersionNumber (default: 3)
343 +poffset (default: 0)
344 +precursorIsolationMargin (default: 0)
345 +precursorWindowSize (default: -1)
346 +ptol (default: 10)
347 +ptolunits (default: ppm)
348 -requireVariableMods (default: false)
349 -variable (default: -)
350 -->
351 <xml name="libexport">
352 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files"/>
353 </xml>
354 </macros>
355 <!--
356 e w t x l param
357 +:+:+:+:+ i
358 +:+:+:+:+ l
359 +:+:+:+:+ f
360
361 +:+:+:+:+ t
362 -:+:-:+:- tp
363 -:+:-:+:+ a
364
365 +:+:+:+:+ o
366
367 +:+:+:+:- acquisition
368 -:+:-:+:- addDecoysToBackground
369 -:+:-:+:- alpha
370 -:+:-:+:- beta
371 -:-:-:-:+ blib
372 -:+:-:+:- dontRunDecoys
373 +:+:+:+:- enzyme
374 +:-:+:-:- expectedPeakWidth
375 +:+:+:+:- filterPeaklists
376 +:+:+:+:+ fixed
377 +:+:+:+:+ foffset
378 +:+:+:+:- frag
379 +:+:+:+:+ ftol
380 +:+:+:+:+ ftolunits
381 +:-:+:-:- lftol
382 +:-:+:-:- lftolunits
383 +:-:-:-:- libexport
384 +:-:+:-:+ localizationModification
385 -:+:-:+:- maxCharge
386 -:+:-:+:- maxLength
387 -:+:-:+:- maxMissedCleavage
388 -:+:-:+:- minCharge
389 -:+:-:+:- minEluteTime
390 +:+:+:+:- minIntensity
391 -:+:-:+:- minLength
392 +:+:+:+:+ minNumOfQuantitativePeaks
393 +:+:+:+:+ minQuantitativeIonNumber
394 +:-:+:-:+ numberOfExtraDecoyLibrariesSearched
395 +:+:+:+:+ numberOfQuantitativePeaks
396 -:+:-:+:- numberOfReportedPeaks
397 -:+:-:+:- numberOfThreadsUsed
398 -:-:-:-:+ percolatorLocation
399 -:+:-:+:- percolatorProteinThreshol
400 +:-:+:-:+ percolatorProteinThreshold
401 +:+:+:+:+ percolatorThreshold
402 +:+:+:+:- percolatorVersionNumber
403 -:-:-:-:+ phospho
404 +:+:+:+:- poffset
405 +:+:+:+:- precursorIsolationMargin
406 +:+:+:+:- precursorWindowSize
407 +:+:+:+:- ptol
408 +:+:+:+:- ptolunits
409 -:+:-:+:- requireVariableMods
410 +:-:+:-:- rtWindowInMin
411 +:-:+:-:- scoringBreadthType
412 -:+:-:+:- variable
413 +:-:+:-:- verifyModificationIons
414 -->