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comparison macros.xml @ 0:56cce1a90b73 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
author computational-metabolomics
date Wed, 27 Nov 2019 14:26:04 -0500
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children 3d6356bcf998
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-1:000000000000 0:56cce1a90b73
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">1.12.0</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="1.42.0" >bioconductor-camera</requirement>
10 <requirement type="package" version="3.8.0" >bioconductor-xcms</requirement>
11 <requirement type="package" version="1.14.0" >bioconductor-mspuritydata</requirement>
12 <requirement type="package" version="1.6.4">r-optparse</requirement>
13 <requirement type="package" version="1.1.1">r-rpostgres</requirement>
14 <requirement type="package" version="0.10.17">r-rmysql</requirement>
15 <yield />
16 </requirements>
17 </xml>
18
19
20 <xml name="offsets">
21 <param argument="--minoffset" type="float" label="minoffset" value="0.5"
22 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
23 100.0 then the range would be from 999.5 to 100.0"/>
24 <param argument="--maxoffset" type="float" label="maxoffset" value="0.5"
25 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is
26 100.0 then the range would be from 100.0 to 100.5"/>
27 </xml>
28 <xml name="general_params">
29 <param argument="--ilim" type="float" value="0.05"
30 label="Threshold to remove peaks below x % of the relative intensity of
31 precursor of interest"
32 help="All peaks less than this percentage of the precursor ion of interest will be
33 removed from the purity calculation, default is 5\% (0.05).
34 Essentially a noise filter to remove peaks that are thought to have either none or
35 very limited impact on the resulting fragmentation spectra."/>
36 <param argument="--iw_norm" type="select" label="Normalisation for isolation efficiency">
37 <option value="gauss" >Gaussian</option>
38 <option value="rcosine" >Raised cosine</option>
39 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
40 <option value="none" selected="true" >No normalisation</option>
41 </param>
42 <conditional name="isotopes">
43 <param argument="--isotopes" type="select" label="Handling of isotopic peaks" >
44 <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
45 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
46 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
47 </param>
48 <when value="keep">
49 </when>
50 <when value="exclude_default">
51 </when>
52 <when value="user">
53 <param argument="--im" type="data" format="tabular" label="Isotope matrix" help="
54 tabular file composing of columns:
55 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
56 'charge', 'relative atomic mass (int)', 'xflag'].
57 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
58 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
59 so we would flag as 0.
60 Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>
61 </when>
62 </conditional>
63 </xml>
64
65
66 <xml name="camera_xcms">
67 <param argument="--camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?"
68 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called
69 xa (or both). The XCMS object is nested within the CAMERA object so either can be used">
70 <option value="xcms" selected="true" >XCMS (xset)</option>
71 <option value="camera" >CAMERA (xa)</option>
72 </param>
73 </xml>
74
75
76 <xml name="fileload">
77 <conditional name="file_load_conditional">
78 <param name="file_load_select" type="select" label="Resubmit your dataset"
79 help="Use only if you get a message which say that your original dataset or
80 dataset collection can not be found the server." >
81 <option value="no" >no need</option>
82 <option value="yes" >yes</option>
83 </param>
84 <when value="no">
85 </when>
86 <when value="yes">
87 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf"
88 multiple="true" label="File(s) from your history containing your chromatograms"
89 help="Select the dataset collection containing the files that were used
90 for processing" />
91 </when>
92 </conditional>
93 </xml>
94
95 <xml name="grp_peaklist">
96 <conditional name="grp_peaklist_opt">
97 <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
98 <option value="yes" >Provide group peaklist </option>
99 <option value="no" selected="true">Use default grouped peaklist</option>
100 </param>
101 <when value="no">
102 </when>
103 <when value="yes">
104 <param argument="--grp_peaklist" type="data" label="grouped peaklist"
105 help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
106 CAMERA annotations" format="tsv,tabular"/>
107 </when>
108 </conditional>
109 </xml>
110
111 <xml name="sm_input" token_ql='Query' token_dblabel="SQLite database" token_ql_shrt="Q"
112 token_user="True" token_mspuritydatalib="False" token_msp="False" token_help="">
113 <conditional name="@QL_SHRT@_dbPth_con">
114 <param argument="--@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" >
115 <option value="sqlite" selected="@USER@" >SQLite database of (LC)-MS/MS data</option>
116 <option value="local_config" selected="@USER@" >Locally configured SQLite, MySQL or PostgreSQL database</option>
117 <option value="msPurityData" selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option>
118 </param>
119 <when value="sqlite">
120 <param argument="--@QL_SHRT@_dbPth" type="data" label="@QL@ SQLite database" format="sqlite" help=""/>
121 </when>
122 <when value="local_config">
123 </when>
124 <when value="msPurityData">
125 </when>
126 </conditional>
127 </xml>
128
129
130 <xml name="filters" token_ql="Query" token_polarity_positive="false" token_ql_shrt="Q"
131 token_sources_select="false" token_instrument_types_select="false">
132
133 <section name="@QL_SHRT@_filters" title="Filters" expanded="False">
134
135 <param argument="--@QL_SHRT@_ppmPrec" type="float" value="5" label="ppm error of the precursor for spectra"/>
136 <param argument="--@QL_SHRT@_ppmProd" type="float" value="10" label="ppm error of the product for spectra"/>
137
138 <conditional name="@QL_SHRT@_raThres_cond">
139 <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/>
140 <when value="true">
141 <param argument="--@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/>
142 </when>
143 <when value="false">
144 </when>
145 </conditional>
146
147 <conditional name="@QL_SHRT@_polarity_cond">
148 <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" />
149 <when value="true">
150 <param argument="--@QL_SHRT@_polarity" type="select" label="Polarity" multiple="true" >
151 <option value="positive" selected="@POLARITY_POSITIVE@">Positive</option>
152 <option value="negative" >Negative</option>
153 <option value="NA" >NA</option>
154 </param>
155 </when>
156 <when value="false">
157 </when>
158 </conditional>
159
160 <conditional name="@QL_SHRT@_purity_cond">
161 <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/>
162 <when value="true">
163 <param argument="--@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6"
164 label="Precursor ion purity threshold"/>
165 </when>
166 <when value="false">
167 </when>
168 </conditional>
169
170 <conditional name="@QL_SHRT@_xcmsGroups_cond">
171 <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/>
172 <when value="true">
173 <param argument="--@QL_SHRT@_xcmsGroups" type="text" value=""
174 label="XCMS group ids of spectra"
175 help="comma seperated list of grpids (correspond to column 'grpid in c_peak_group'))
176 e.g '12,27,30'" />
177 </when>
178 <when value="false">
179 </when>
180 </conditional>
181
182
183 <conditional name="@QL_SHRT@_pids_cond">
184 <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/>
185 <when value="true">
186 <param argument="--@QL_SHRT@_pids" type="text" value=""
187 label="pids of spectra (correspond to column 'pid; in s_peak_meta)"
188 help="comma seperated list of pids (correspond to column 'pid; in s_peak_meta))
189 e.g '3001,5561'" />
190 </when>
191 <when value="false">
192 </when>
193 </conditional>
194
195
196 <conditional name="@QL_SHRT@_rtrange_cond">
197 <param name="@QL_SHRT@_rtrange_bool" type="boolean"
198 label="Filter on retention time range?"
199 help="Filter the spectra between two points of retention time range"/>
200 <when value="true">
201 <param argument="--@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)"
202 type="float" value="0" help=""/>
203 <param argument="--@QL_SHRT@_rtrangeMax" label="Maximum retention time range (seconds)"
204 type="float" value="3000" help=""/>
205 </when>
206 <when value="false">
207 </when>
208 </conditional>
209
210
211
212 <conditional name="@QL_SHRT@_accessions_cond">
213 <param name="@QL_SHRT@_accessions_bool" type="boolean"
214 label="Filter on accessions?"
215 help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/>
216 <when value="true">
217 <param argument="--@QL_SHRT@_accessions" type="text" value=""
218 label="Spectra accessions"
219 help="Comma seperated list of accessions))
220 e.g 'AC000001,BS001003,LIT00001'" />
221 </when>
222 <when value="false">
223 </when>
224 </conditional>
225
226
227 <conditional name="@QL_SHRT@_sources_cond">
228 <param name="@QL_SHRT@_sources_bool" type="boolean"
229 label="Filter on sources?" help="" value="@SOURCES_SELECT@" />
230 <when value="true">
231 <param argument="--@QL_SHRT@_sources" type="select" multiple="true"
232 help="@QL_SHRT@ The default internal SQLite database of library (reference) spectra
233 contains fragmentation spectra from MassBank, LipidBlast and GNPS. A copy is
234 available from here:
235 https://bioconductor.org/packages/release/data/experiment/html/msPurityData.html" >
236 <option value="massbank" selected="true">MassBank from MoNa</option>
237 <option value="gnps" selected="true">GNPS</option>
238 <option value="hmdb" selected="true">HMDB</option>
239 <option value="lipidblast" selected="true">LipidBlast</option>
240 </param>
241 <param name="@QL_SHRT@_sourcesUser" type="text" label="Sources - user specific" value=""
242 help="comma seperated list of additional sources (e.g. if the user has other
243 sources - like there own personal library)
244 e.g 'LIPIDS_03052019,HILIC_03052019'" />
245 </when>
246 <when value="false">
247 </when>
248 </conditional>
249 <conditional name="@QL_SHRT@_instrumentTypes_cond">
250 <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean"
251 value="@INSTRUMENT_TYPES_SELECT@"
252 label="Filter on instrument type?" help="" />
253 <when value="true">
254 <param argument="--@QL_SHRT@_instrumentTypes" type="select" multiple="true"
255 help="" >
256 <option value="APCI-ITFT" selected="true" >APCI-ITFT</option>
257 <option value="APCI-ITTOF" selected="true" >APCI-ITTOF</option>
258 <option value="CE-ESI-TOF" selected="true" >CE-ESI-TOF</option>
259 <option value="CI-B">CI-B</option>
260 <option value="EI-B">EI-B</option>
261 <option value="EI-EBEB">EI-EBEB</option>
262 <option value="ESI-ITFT" selected="true" >ESI-ITFT</option>
263 <option value="ESI-ITTOF" selected="true" >ESI-ITTOF</option>
264 <option value="ESI-QFT" selected="true" >ESI-QFT</option>
265 <option value="ESI-QTOF" selected="true" >ESI-QTOF</option>
266 <option value="ESI-TOF" selected="true" >ESI-TOF</option>
267 <option value="FAB-B">FAB-B</option>
268 <option value="FAB-BE">FAB-BE</option>
269 <option value="FAB-EB">FAB-EB</option>
270 <option value="FAB-EBEB">FAB-EBEB</option>
271 <option value="FAB-EBEB">FD-B</option>
272 <option value="FI-B">FI-B</option>
273 <option value="Flow-injection QqQ/MS">Flow-injection QqQ/MS</option>
274 <option value="GC-EI-Q">GC-EI-Q</option>
275 <option value="GC-EI-QQ">GC-EI-QQ</option>
276 <option value="GC-EI-TOF">GC-EI-TOF</option>
277 <option value="GC-MS">GC-MS</option>
278 <option value="Hybrid FT">Hybrid FT</option>
279 <option value="in source CID" selected="true" >in source CID</option>
280 <option value="In-silico QTOF" selected="true" >In-silico QTOF</option>
281 <option value="Ion trap" selected="true" >Ion trap</option>
282 <option value="LC-APCI-ITFT" selected="true" >LC-APCI-ITFT</option>
283 <option value="LC-APCI-QTOF" selected="true" >LC-APCI-QTOF</option>
284 <option value="LC-APCI-Q" selected="true">LC-APCI-Q</option>
285 <option value="LC-APPI-QQ">LC-APPI-QQ</option>
286 <option value="LC-ESI-IT" selected="true">LC-ESI-IT</option>
287 <option value="LC-ESI-ITFT" selected="true">LC-ESI-ITFT</option>
288 <option value="LC-ESI-ITTOF" selected="true">LC-ESI-ITTOF</option>
289 <option value="LC-ESI-Q" selected="true">LC-ESI-Q</option>
290 <option value="LC-ESI-QFT" selected="true">LC-ESI-QFT</option>
291 <option value="LC-ESI-QIT" selected="true">LC-ESI-QIT</option>
292 <option value="LC-ESI-QQ" selected="true">LC-ESI-QQ</option>
293 <option value="LC-ESI-QTOF" selected="true">LC-ESI-QTOF</option>
294 <option value="LC-ESI-TOF" selected="true">LC-ESI-TOF</option>
295 <option value="LC-Q-TOF/MS" selected="true">LC-Q-TOF/MS</option>
296 <option value="LC-QTOF" selected="true">LC-QTOF</option>
297 <option value="Linear Ion Trap" selected="true">Linear Ion Trap</option>
298 <option value="LIT" selected="true">LIT</option>
299 <option value="MALDI-QIT" selected="true">MALDI-QIT</option>
300 <option value="MALDI-TOF" selected="true">MALDI-TOF</option>
301 <option value="MALDI-TOFTOF" selected="true">MALDI-TOFTOF</option>
302 <option value="orbitrap" selected="true">orbitrap</option>
303 <option value="QIT" selected="true">QIT</option>
304 <option value="QIT-FT" selected="true">QIT-FT</option>
305 <option value="QIT-TOF" selected="true">QIT-TOF</option>
306 <option value="QqQ" selected="true">QqQ</option>
307 <option value="Q-TOF" selected="true">Q-TOF</option>
308 <option value="Quattro_QQQ" selected="true">Quattro_QQQ</option>
309 <option value="none">None</option>
310 </param>
311 <param argument="--@QL_SHRT@_instrumentTypesUser" type="text" value=""
312 help="Types of the instruments to be included in the search. Use a comma to
313 separate the instrument types or leave empty to ignore filter."/>
314 </when>
315 <when value="false">
316 </when>
317 </conditional>
318 <conditional name="@QL_SHRT@_instruments_cond">
319 <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" />
320 <when value="true">
321 <param argument="--@QL_SHRT@_instruments" type="text" value=""
322 help="Known instrument names to filter on. Use a comma to
323 separate the instrument types or leave empty to ignore filter."/>
324 </when>
325 <when value="false">
326 </when>
327 </conditional>
328
329
330
331 <conditional name="@QL_SHRT@_spectraTypes_cond">
332 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
333 help="" />
334 <when value="true">
335 <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" >
336 <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
337 <option value="av_inter">Averaged inter spectra</option>
338 <option value="av_intra">Averaged intra spectra </option>
339 <option value="scans">All individual scans</option>
340 <option value="NA">Not applicable/defined</option>
341 </param>
342 </when>
343 <when value="false">
344 </when>
345 </conditional>
346
347 <param argument="--@QL_SHRT@_spectraFilter" type="boolean" checked="true"
348 label="Ignore any peaks flagged in the spectra in previous stages?"
349 help="" />
350
351 </section>
352 </xml>
353
354
355
356
357 <xml name="citations">
358 <citations>
359 <citation type="doi">10.1021/acs.analchem.6b04358</citation>
360 <yield />
361 </citations>
362 </xml>
363
364 </macros>