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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:17:52 +0000
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-1:000000000000 0:353d48ece635
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">1.16.2</token>
4 <token name="@GALAXY_TOOL_VERSION@">0</token>
5
6 <xml name="requirements">
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement>
9 <requirement type="package" version="1.46.0" >bioconductor-camera</requirement>
10 <requirement type="package" version="3.12.0" >bioconductor-xcms</requirement>
11 <requirement type="package" version="1.16.0" >bioconductor-mspuritydata</requirement>
12 <requirement type="package" version="1.6.6">r-optparse</requirement>
13 <requirement type="package" version="1.3.1">r-rpostgres</requirement>
14 <requirement type="package" version="0.10.21">r-rmysql</requirement>
15 <yield />
16 </requirements>
17 </xml>
18
19 <xml name="text-adduct-regex-validator">
20 <validator type="regex" message="Value may include alphanumeric characters, white space, commas, +, -, [ or ] ">[A-Za-z0-9,\[\] \+\-]+</validator>
21 </xml>
22
23 <xml name="offsets">
24 <param argument="--minoffset" type="float" label="minoffset" value="0.5"
25 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
26 100.0 then the range would be from 99.5 to 100.0"/>
27 <param argument="--maxoffset" type="float" label="maxoffset" value="0.5"
28 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is
29 100.0 then the range would be from 100.0 to 100.5"/>
30 </xml>
31 <xml name="general_params">
32 <param argument="--ilim" type="float" value="0.05"
33 label="Threshold to remove peaks below x % of the relative intensity of
34 precursor of interest"
35 help="All peaks less than this percentage of the precursor ion of interest will be
36 removed from the purity calculation, default is 5\% (0.05).
37 Essentially a noise filter to remove peaks that are thought to have either none or
38 very limited impact on the resulting fragmentation spectra."/>
39 <param argument="--iw_norm" type="select" label="Normalisation for isolation efficiency">
40 <option value="gauss" >Gaussian</option>
41 <option value="rcosine" >Raised cosine</option>
42 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
43 <option value="none" selected="true" >No normalisation</option>
44 </param>
45 <conditional name="isotopes">
46 <param argument="--isotopes" type="select" label="Handling of isotopic peaks" >
47 <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
48 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
49 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
50 </param>
51 <when value="keep">
52 </when>
53 <when value="exclude_default">
54 </when>
55 <when value="user">
56 <param argument="--im" type="data" format="tabular" label="Isotope matrix" help="
57 tabular file composing of columns:
58 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
59 'charge', 'relative atomic mass (int)', 'xflag'].
60 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
61 e.g. for c12 to c13, the c13 is less abundant so we flag as 1 for Li6 to Li7, the Li7 is more abundant
62 so we would flag as 0.
63 Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>
64 </when>
65 </conditional>
66 </xml>
67
68
69 <xml name="camera_xcms">
70 <param argument="--camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?"
71 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called
72 xa (or both). The XCMS object is nested within the CAMERA object so either can be used">
73 <option value="xcms" selected="true" >XCMS (xset)</option>
74 <option value="camera" >CAMERA (xa)</option>
75 </param>
76 </xml>
77
78
79 <xml name="fileload">
80 <conditional name="file_load_conditional">
81 <param name="file_load_select" type="select" label="Resubmit your dataset"
82 help="Use only if you get a message which say that your original dataset or
83 dataset collection can not be found the server." >
84 <option value="no" >no need</option>
85 <option value="yes" >yes</option>
86 </param>
87 <when value="no">
88 </when>
89 <when value="yes">
90 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf"
91 multiple="true" label="File(s) from your history containing your chromatograms"
92 help="Select the dataset collection containing the files that were used
93 for processing" />
94 </when>
95 </conditional>
96 </xml>
97
98 <xml name="grp_peaklist">
99 <conditional name="grp_peaklist_opt">
100 <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
101 <option value="yes" >Provide group peaklist </option>
102 <option value="no" selected="true">Use default grouped peaklist</option>
103 </param>
104 <when value="no">
105 </when>
106 <when value="yes">
107 <param argument="--grp_peaklist" type="data" label="grouped peaklist"
108 help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
109 CAMERA annotations" format="tsv,tabular"/>
110 </when>
111 </conditional>
112 </xml>
113
114 <xml name="sm_input" token_ql='Query' token_dblabel="SQLite database" token_ql_shrt="Q"
115 token_user="True" token_mspuritydatalib="False" token_msp="False" token_help="">
116 <conditional name="@QL_SHRT@_dbPth_con">
117 <param argument="--@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" >
118 <option value="sqlite" selected="@USER@" >SQLite database of (LC)-MS/MS data</option>
119 <option value="local_config" selected="@USER@" >Locally configured SQLite, MySQL or PostgreSQL database</option>
120 <option value="msPurityData" selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option>
121 </param>
122 <when value="sqlite">
123 <param argument="--@QL_SHRT@_dbPth" type="data" label="@QL@ SQLite database" format="sqlite" help=""/>
124 </when>
125 <when value="local_config">
126 </when>
127 <when value="msPurityData">
128 </when>
129 </conditional>
130 </xml>
131
132
133 <xml name="filters" token_ql="Query" token_polarity_positive="false" token_ql_shrt="Q"
134 token_sources_select="false" token_instrument_types_select="false">
135
136 <section name="@QL_SHRT@_filters" title="Filters" expanded="False">
137
138 <param argument="--@QL_SHRT@_ppmPrec" type="float" value="5" label="ppm error of the precursor for spectra"/>
139 <param argument="--@QL_SHRT@_ppmProd" type="float" value="10" label="ppm error of the product for spectra"/>
140
141 <conditional name="@QL_SHRT@_raThres_cond">
142 <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/>
143 <when value="true">
144 <param argument="--@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/>
145 </when>
146 <when value="false">
147 </when>
148 </conditional>
149
150 <conditional name="@QL_SHRT@_polarity_cond">
151 <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" />
152 <when value="true">
153 <param argument="--@QL_SHRT@_polarity" type="select" label="Polarity" multiple="true" >
154 <option value="positive" selected="@POLARITY_POSITIVE@">Positive</option>
155 <option value="negative" >Negative</option>
156 <option value="NA" >NA</option>
157 </param>
158 </when>
159 <when value="false">
160 </when>
161 </conditional>
162
163 <conditional name="@QL_SHRT@_purity_cond">
164 <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/>
165 <when value="true">
166 <param argument="--@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6"
167 label="Precursor ion purity threshold"/>
168 </when>
169 <when value="false">
170 </when>
171 </conditional>
172
173 <conditional name="@QL_SHRT@_xcmsGroups_cond">
174 <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/>
175 <when value="true">
176 <param argument="--@QL_SHRT@_xcmsGroups" type="text" value=""
177 label="XCMS group ids of spectra"
178 help="comma seperated list of grpids (correspond to column 'grpid in c_peak_group'))
179 e.g '12,27,30'" />
180 </when>
181 <when value="false">
182 </when>
183 </conditional>
184
185
186 <conditional name="@QL_SHRT@_pids_cond">
187 <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/>
188 <when value="true">
189 <param argument="--@QL_SHRT@_pids" type="text" value=""
190 label="pids of spectra (correspond to column 'pid; in s_peak_meta)"
191 help="comma seperated list of pids (correspond to column 'pid; in s_peak_meta))
192 e.g '3001,5561'" />
193 </when>
194 <when value="false">
195 </when>
196 </conditional>
197
198
199 <conditional name="@QL_SHRT@_rtrange_cond">
200 <param name="@QL_SHRT@_rtrange_bool" type="boolean"
201 label="Filter on retention time range?"
202 help="Filter the spectra between two points of retention time range"/>
203 <when value="true">
204 <param argument="--@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)"
205 type="float" value="0" help=""/>
206 <param argument="--@QL_SHRT@_rtrangeMax" label="Maximum retention time range (seconds)"
207 type="float" value="3000" help=""/>
208 </when>
209 <when value="false">
210 </when>
211 </conditional>
212
213
214
215 <conditional name="@QL_SHRT@_accessions_cond">
216 <param name="@QL_SHRT@_accessions_bool" type="boolean"
217 label="Filter on accessions?"
218 help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/>
219 <when value="true">
220 <param argument="--@QL_SHRT@_accessions" type="text" value=""
221 label="Spectra accessions"
222 help="Comma seperated list of accessions))
223 e.g 'AC000001,BS001003,LIT00001'" />
224 </when>
225 <when value="false">
226 </when>
227 </conditional>
228
229
230 <conditional name="@QL_SHRT@_sources_cond">
231 <param name="@QL_SHRT@_sources_bool" type="boolean"
232 label="Filter on sources?" help="" value="@SOURCES_SELECT@" />
233 <when value="true">
234 <param argument="--@QL_SHRT@_sources" type="select" multiple="true"
235 help="@QL_SHRT@ The default internal SQLite database of library (reference) spectra
236 contains fragmentation spectra from MassBank, LipidBlast and GNPS. A copy is
237 available from here:
238 https://bioconductor.org/packages/release/data/experiment/html/msPurityData.html" >
239 <option value="massbank" selected="true">MassBank from MoNa</option>
240 <option value="gnps" selected="true">GNPS</option>
241 <option value="hmdb" selected="true">HMDB</option>
242 <option value="lipidblast" selected="true">LipidBlast</option>
243 </param>
244 <param name="@QL_SHRT@_sourcesUser" type="text" label="Sources - user specific" value=""
245 help="comma seperated list of additional sources (e.g. if the user has other
246 sources - like there own personal library)
247 e.g 'LIPIDS_03052019,HILIC_03052019'" />
248 </when>
249 <when value="false">
250 </when>
251 </conditional>
252 <conditional name="@QL_SHRT@_instrumentTypes_cond">
253 <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean"
254 value="@INSTRUMENT_TYPES_SELECT@"
255 label="Filter on instrument type?" help="" />
256 <when value="true">
257 <param argument="--@QL_SHRT@_instrumentTypes" type="select" multiple="true"
258 help="" >
259 <option value="APCI-ITFT" selected="true" >APCI-ITFT</option>
260 <option value="APCI-ITTOF" selected="true" >APCI-ITTOF</option>
261 <option value="CE-ESI-TOF" selected="true" >CE-ESI-TOF</option>
262 <option value="CI-B">CI-B</option>
263 <option value="EI-B">EI-B</option>
264 <option value="EI-EBEB">EI-EBEB</option>
265 <option value="ESI-ITFT" selected="true" >ESI-ITFT</option>
266 <option value="ESI-ITTOF" selected="true" >ESI-ITTOF</option>
267 <option value="ESI-QFT" selected="true" >ESI-QFT</option>
268 <option value="ESI-QTOF" selected="true" >ESI-QTOF</option>
269 <option value="ESI-TOF" selected="true" >ESI-TOF</option>
270 <option value="FAB-B">FAB-B</option>
271 <option value="FAB-BE">FAB-BE</option>
272 <option value="FAB-EB">FAB-EB</option>
273 <option value="FAB-EBEB">FAB-EBEB</option>
274 <option value="FAB-EBEB">FD-B</option>
275 <option value="FI-B">FI-B</option>
276 <option value="Flow-injection QqQ/MS">Flow-injection QqQ/MS</option>
277 <option value="GC-EI-Q">GC-EI-Q</option>
278 <option value="GC-EI-QQ">GC-EI-QQ</option>
279 <option value="GC-EI-TOF">GC-EI-TOF</option>
280 <option value="GC-MS">GC-MS</option>
281 <option value="Hybrid FT">Hybrid FT</option>
282 <option value="in source CID" selected="true" >in source CID</option>
283 <option value="In-silico QTOF" selected="true" >In-silico QTOF</option>
284 <option value="Ion trap" selected="true" >Ion trap</option>
285 <option value="LC-APCI-ITFT" selected="true" >LC-APCI-ITFT</option>
286 <option value="LC-APCI-QTOF" selected="true" >LC-APCI-QTOF</option>
287 <option value="LC-APCI-Q" selected="true">LC-APCI-Q</option>
288 <option value="LC-APPI-QQ">LC-APPI-QQ</option>
289 <option value="LC-ESI-IT" selected="true">LC-ESI-IT</option>
290 <option value="LC-ESI-ITFT" selected="true">LC-ESI-ITFT</option>
291 <option value="LC-ESI-ITTOF" selected="true">LC-ESI-ITTOF</option>
292 <option value="LC-ESI-Q" selected="true">LC-ESI-Q</option>
293 <option value="LC-ESI-QFT" selected="true">LC-ESI-QFT</option>
294 <option value="LC-ESI-QIT" selected="true">LC-ESI-QIT</option>
295 <option value="LC-ESI-QQ" selected="true">LC-ESI-QQ</option>
296 <option value="LC-ESI-QTOF" selected="true">LC-ESI-QTOF</option>
297 <option value="LC-ESI-TOF" selected="true">LC-ESI-TOF</option>
298 <option value="LC-Q-TOF/MS" selected="true">LC-Q-TOF/MS</option>
299 <option value="LC-QTOF" selected="true">LC-QTOF</option>
300 <option value="Linear Ion Trap" selected="true">Linear Ion Trap</option>
301 <option value="LIT" selected="true">LIT</option>
302 <option value="MALDI-QIT" selected="true">MALDI-QIT</option>
303 <option value="MALDI-TOF" selected="true">MALDI-TOF</option>
304 <option value="MALDI-TOFTOF" selected="true">MALDI-TOFTOF</option>
305 <option value="orbitrap" selected="true">orbitrap</option>
306 <option value="QIT" selected="true">QIT</option>
307 <option value="QIT-FT" selected="true">QIT-FT</option>
308 <option value="QIT-TOF" selected="true">QIT-TOF</option>
309 <option value="QqQ" selected="true">QqQ</option>
310 <option value="Q-TOF" selected="true">Q-TOF</option>
311 <option value="Quattro_QQQ" selected="true">Quattro_QQQ</option>
312 <option value="none">None</option>
313 </param>
314 <param argument="--@QL_SHRT@_instrumentTypesUser" type="text" value=""
315 help="Types of the instruments to be included in the search. Use a comma to
316 separate the instrument types or leave empty to ignore filter."/>
317 </when>
318 <when value="false">
319 </when>
320 </conditional>
321 <conditional name="@QL_SHRT@_instruments_cond">
322 <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" />
323 <when value="true">
324 <param argument="--@QL_SHRT@_instruments" type="text" value=""
325 help="Known instrument names to filter on. Use a comma to
326 separate the instrument types or leave empty to ignore filter."/>
327 </when>
328 <when value="false">
329 </when>
330 </conditional>
331
332
333
334 <conditional name="@QL_SHRT@_spectraTypes_cond">
335 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
336 help="" />
337 <when value="true">
338 <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" >
339 <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
340 <option value="inter">Averaged inter spectra</option>
341 <option value="intra">Averaged intra spectra </option>
342 <option value="scans">All individual scans</option>
343 <option value="NA">Not applicable/defined</option>
344 </param>
345 </when>
346 <when value="false">
347 </when>
348 </conditional>
349
350 <param argument="--@QL_SHRT@_spectraFilter" type="boolean" checked="true"
351 label="Ignore any peaks flagged in the spectra in previous stages?"
352 help="" />
353
354 </section>
355 </xml>
356
357
358
359
360 <xml name="citations">
361 <citations>
362 <citation type="doi">10.1021/acs.analchem.6b04358</citation>
363 <yield />
364 </citations>
365 </xml>
366
367 </macros>