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comparison macros.xml @ 0:fc9bb7e49a3a draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 09:02:25 -0400
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children 92dbd3a31caf
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-1:000000000000 0:fc9bb7e49a3a
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="1.10.0" >bioconductor-mspurity</requirement>
6 <yield />
7 </requirements>
8 </xml>
9 <xml name="offsets">
10 <param name="minoffset" type="float" label="minoffset" value="0.5" argument='--minoffset'
11 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
12 100.0 then the range would be from 999.5 to 100.0"/>
13 <param name="maxoffset" type="float" label="maxoffset" value="0.5" argument='--maxoffset'
14 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is
15 100.0 then the range would be from 100.0 to 100.5"/>
16 </xml>
17 <xml name="general_params">
18 <param name="ilim" type="float" value="0.05" argument='--ilim'
19 label="Threshold to remove peaks below x % of the relative intensity of
20 precursor of interest"
21 help="All peaks less than this percentage of the precursor ion of interest will be
22 removed from the purity calculation, default is 5\% (0.05).
23 Essentially a noise filter to remove peaks that are thought to have either none or
24 very limited impact on the resulting fragmentation spectra."/>
25 <param name="iw_norm" type="select" label="Normalisation for isolation efficiency">
26 <option value="gauss" >Gaussian</option>
27 <option value="rcosine" >Raised cosine</option>
28 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
29 <option value="none" selected="true" >No normalisation</option>
30 </param>
31 <conditional name="isotopes">
32 <param name="isotopes" type="select" label="Handling of isotopic peaks" >
33 <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
34 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
35 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
36 </param>
37 <when value="keep">
38 </when>
39 <when value="exclude_default">
40 </when>
41 <when value="user">
42 <param name="im" type="data" format="tabular" label="Isotope matrix" help="
43 tabular file composing of columns:
44 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
45 'charge', 'relative atomic mass (int)', 'xflag'].
46 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
47 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
48 so we would flag as 0.
49 Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>
50 </when>
51 </conditional>
52 </xml>
53
54
55 <xml name="camera_xcms">
56 <param name="camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?"
57 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called
58 xa (or both). The XCMS object is nested within the CAMERA object so either can be used">
59 <option value="xcms" selected="true" >XCMS (xset)</option>
60 <option value="camera" >CAMERA (xa)</option>
61 </param>
62 </xml>
63
64
65 <xml name="fileload">
66 <conditional name="file_load_conditional">
67 <param name="file_load_select" type="select" label="Resubmit your dataset"
68 help="Use only if you get a message which say that your original dataset or
69 dataset collection can not be found the server." >
70 <option value="no" >no need</option>
71 <option value="yes" >yes</option>
72 </param>
73 <when value="no">
74 </when>
75 <when value="yes">
76 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf"
77 multiple="true" label="File(s) from your history containing your chromatograms"
78 help="Select the dataset collection containing the files that were used
79 for processing" />
80 </when>
81 </conditional>
82 </xml>
83
84 <xml name="grp_peaklist">
85 <conditional name="grp_peaklist_opt">
86 <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
87 <option value="yes" >Provide group peaklist </option>
88 <option value="no" selected="true">Use default grouped peaklist</option>
89 </param>
90 <when value="no">
91 </when>
92 <when value="yes">
93 <param type="data" name="grp_peaklist" label="grouped peaklist"
94 help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
95 CAMERA annotations" format="tsv,tabular"/>
96 </when>
97 </conditional>
98 </xml>
99
100
101 <xml name="sm_input" token_ql='Query' token_dblabel="SQLite database" token_ql_shrt="Q"
102 token_user="True" token_mspuritydatalib="False" token_msp="False" token_help="">
103 <conditional name="@QL_SHRT@_dbPth_con">
104 <param name="@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" >
105 <option value="userdb" selected="@USER@" >SQLite database of (LC)-MS/MS data</option>
106 <option value="msPurityData" selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option>
107 <option value="msp" >MSP file (SQLite database will be created using using msp2db)</option>
108 </param>
109 <when value="userdb">
110 <param type="data" name="@QL_SHRT@_dbPth" label="@QL@ SQLite database" format="sqlite" help=""/>
111 </when>
112 <when value="msp">
113 <param type="data" name="@QL_SHRT@_msp" label="@QL@ MSP file" format="msp" help=""/>
114 </when>
115
116 <when value="msPurityData">
117 </when>
118 </conditional>
119 </xml>
120
121
122 <xml name="filters" token_ql="Query" token_polarity_positive="false" token_ql_shrt="Q"
123 token_sources_select="false" token_instrument_types_select="false">
124
125 <section name="@QL_SHRT@_filters" title="Filters" expanded="False">
126
127 <param name="@QL_SHRT@_ppmPrec" type="float" value="5" label="ppm error of the precursor for spectra"/>
128 <param name="@QL_SHRT@_ppmProd" type="float" value="10" label="ppm error of the product for spectra"/>
129
130 <conditional name="@QL_SHRT@_raThres_cond">
131 <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/>
132 <when value="true">
133 <param name="@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/>
134 </when>
135 <when value="false">
136 </when>
137 </conditional>
138
139 <conditional name="@QL_SHRT@_polarity_cond">
140 <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" />
141 <when value="true">
142 <param name="@QL_SHRT@_polarity" type="select" label="Polarity" multiple="true" >
143 <option value="positive" selected="@POLARITY_POSITIVE@">Positive</option>
144 <option value="negative" >Negative</option>
145 <option value="NA" >NA</option>
146 </param>
147 </when>
148 <when value="false">
149 </when>
150 </conditional>
151
152 <conditional name="@QL_SHRT@_purity_cond">
153 <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/>
154 <when value="true">
155 <param name="@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6"
156 label="Precursor ion purity threshold"/>
157 </when>
158 <when value="false">
159 </when>
160 </conditional>
161
162 <conditional name="@QL_SHRT@_xcmsGroups_cond">
163 <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/>
164 <when value="true">
165 <param name="@QL_SHRT@_xcmsGroups" type="text" value=""
166 label="XCMS group ids of spectra"
167 help="comma seperated list of grpids (correspond to column 'grpid in c_peak_group'))
168 e.g '12,27,30'" />
169 </when>
170 <when value="false">
171 </when>
172 </conditional>
173
174
175 <conditional name="@QL_SHRT@_pids_cond">
176 <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/>
177 <when value="true">
178 <param name="@QL_SHRT@_pids" type="text" value=""
179 label="pids of spectra (correspond to column 'pid; in s_peak_meta)"
180 help="comma seperated list of pids (correspond to column 'pid; in s_peak_meta))
181 e.g '3001,5561'" />
182 </when>
183 <when value="false">
184 </when>
185 </conditional>
186
187
188 <conditional name="@QL_SHRT@_rtrange_cond">
189 <param name="@QL_SHRT@_rtrange_bool" type="boolean"
190 label="Filter on retention time range?"
191 help="Filter the spectra between two points of retention time range"/>
192 <when value="true">
193 <param name="@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)"
194 type="float" value="0" help=""/>
195 <param name="@QL_SHRT@_rtrangeMax" label="Maximum retention time range (seconds)"
196 type="float" value="3000" help=""/>
197 </when>
198 <when value="false">
199 </when>
200 </conditional>
201
202
203
204 <conditional name="@QL_SHRT@_accessions_cond">
205 <param name="@QL_SHRT@_accessions_bool" type="boolean"
206 label="Filter on accessions?"
207 help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/>
208 <when value="true">
209 <param name="@QL_SHRT@_accessions" type="text" value=""
210 label="Spectra accessions"
211 help="Comma seperated list of accessions))
212 e.g 'AC000001,BS001003,LIT00001'" />
213 </when>
214 <when value="false">
215 </when>
216 </conditional>
217
218
219 <conditional name="@QL_SHRT@_sources_cond">
220 <param name="@QL_SHRT@_sources_bool" type="boolean"
221 label="Filter on sources?" help="" value="@SOURCES_SELECT@" />
222 <when value="true">
223 <param name="@QL_SHRT@_sources" type="select" multiple="true"
224 help="@QL_SHRT@ The default internal SQLite database of library (reference) spectra
225 contains fragmentation spectra from MassBank, LipidBlast and GNPS. A copy is
226 available from here:
227 https://bioconductor.org/packages/release/data/experiment/html/msPurityData.html" >
228 <option value="massbank" selected="true">MassBank from MoNa</option>
229 <option value="gnps" selected="true">GNPS</option>
230 <option value="hmdb" selected="true">HMDB</option>
231 <option value="lipidblast" selected="true">LipidBlast</option>
232 </param>
233 <param name="@QL_SHRT@_sourcesUser" type="text" label="Sources - user specific" value=""
234 help="comma seperated list of additional sources (e.g. if the user has other
235 sources - like there own personal library)
236 e.g 'LIPIDS_03052019,HILIC_03052019'" />
237 </when>
238 <when value="false">
239 </when>
240 </conditional>
241 <conditional name="@QL_SHRT@_instrumentTypes_cond">
242 <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean"
243 value="@INSTRUMENT_TYPES_SELECT@"
244 label="Filter on instrument type?" help="" />
245 <when value="true">
246 <param name="@QL_SHRT@_instrumentTypes" type="select" multiple="true"
247 help="" >
248 <option value="APCI-ITFT">APCI-ITFT</option>
249 <option value="CE-ESI-TOF" selected="true">CE-ESI-TOF</option>
250 <option value="CI-B">CI-B</option>
251 <option value="EI-B">EI-B</option>
252 <option value="EI-EBEB">EI-EBEB</option>
253 <option value="ESI-ITFT" selected="true">ESI-ITFT</option>
254 <option value="ESI-ITTOF" selected="true">ESI-ITTOF</option>
255 <option value="ESI-QTOF" selected="true">ESI-QTOF</option>
256 <option value="FAB-B">FAB-B</option>
257 <option value="FAB-BE-MS">FAB-BE-MS</option>
258 <option value="FAB-EB">FAB-EB</option>
259 <option value="FAB-EBEB">FAB-EBEB</option>
260 <option value="FI-B">FI-B</option>
261 <option value="GC-EI-Q">GC-EI-Q</option>
262 <option value="GC-EI-QQ">GC-EI-QQ</option>
263 <option value="GC-EI-TOF">GC-EI-TOF</option>
264 <option value="LC-APCI-QTOF">LC-APCI-QTOF</option>
265 <option value="LC-APPI-QQ">LC-APPI-QQ</option>
266 <option value="LC-ESI-IT" selected="true">LC-ESI-IT</option>
267 <option value="LC-ESI-ITFT" selected="true">LC-ESI-ITFT</option>
268 <option value="LC-ESI-ITTOF" selected="true">LC-ESI-ITTOF</option>
269 <option value="LC-ESI-Q">LC-ESI-Q</option>
270 <option value="LC-ESI-QFT" selected="true" >LC-ESI-QFT</option>
271 <option value="LC-ESI-QIT" selected="true">LC-ESI-QIT</option>
272 <option value="LC-ESI-QQ" selected="true">LC-ESI-QQ</option>
273 <option value="LC-ESI-QTOF" selected="true">LC-ESI-QTOF</option>
274 <option value="LC-ESI-TOF" selected="true">LC-ESI-TOF</option>
275 <option value="MALDI-QIT">MALDI-QIT</option>
276 <option value="MALDI-TOF">MALDI-TOF</option>
277 <option value="ALDI-TOFTOF">ALDI-TOFTOF</option>
278 <option value="none">None</option>
279 </param>
280 <param name="@QL_SHRT@_instrumentTypesUser" type="text" value=""
281 help="Types of the instruments to be included in the search. Use a comma to
282 separate the instrument types or leave empty to ignore filter."/>
283 </when>
284 <when value="false">
285 </when>
286 </conditional>
287 <conditional name="@QL_SHRT@_instruments_cond">
288 <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" />
289 <when value="true">
290 <param name="@QL_SHRT@_instruments" type="text" value=""
291 help="Known instrument names to filter on. Use a comma to
292 separate the instrument types or leave empty to ignore filter."/>
293 </when>
294 <when value="false">
295 </when>
296 </conditional>
297
298
299
300 <conditional name="@QL_SHRT@_spectraTypes_cond">
301 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
302 help="" />
303 <when value="true">
304 <param name="@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" >
305 <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
306 <option value="av_inter">Averaged inter spectra</option>
307 <option value="av_intra">Averaged intra spectra </option>
308 <option value="scans">All individual scans</option>
309 <option value="NA">Not applicable/defined</option>
310 </param>
311 </when>
312 <when value="false">
313 </when>
314 </conditional>
315
316 <param name="@QL_SHRT@_spectraFilter" type="boolean" checked="true"
317 label="Ignore any peaks flagged in the spectra in previous stages?"
318 help="" />
319
320 </section>
321 </xml>
322
323
324
325
326 <xml name="citations">
327 <citations>
328 <citation type="doi">10.1021/acs.analchem.6b04358</citation>
329 <yield />
330 </citations>
331 </xml>
332
333 </macros>