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comparison macros.xml @ 11:7e4a5ce0877d draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3
author tomnl
date Thu, 27 Jun 2019 12:28:15 -0400
parents b74303b60450
children 2c8b5a640a04
comparison
equal deleted inserted replaced
10:b74303b60450 11:7e4a5ce0877d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.11.3</token>
4 <token name="@GALAXY_TOOL_VERSION@">0.2.5</token>
5
3 <xml name="requirements"> 6 <xml name="requirements">
4 <requirements> 7 <requirements>
5 <requirement type="package" version="1.11.2" >bioconductor-mspurity</requirement> 8 <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement>
6 <yield /> 9 <yield />
7 </requirements> 10 </requirements>
8 </xml> 11 </xml>
12
13
9 <xml name="offsets"> 14 <xml name="offsets">
10 <param name="minoffset" type="float" label="minoffset" value="0.5" argument='--minoffset' 15 <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 16 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"/> 17 100.0 then the range would be from 999.5 to 100.0"/>
13 <param name="maxoffset" type="float" label="maxoffset" value="0.5" argument='--maxoffset' 18 <param name="maxoffset" type="float" label="maxoffset" value="0.5" argument='--maxoffset'
94 help="User supplied grouped peaklist to add to the database (if additional columns required e.g. 99 help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
95 CAMERA annotations" format="tsv,tabular"/> 100 CAMERA annotations" format="tsv,tabular"/>
96 </when> 101 </when>
97 </conditional> 102 </conditional>
98 </xml> 103 </xml>
99 104
100 105
101 <xml name="sm_input" token_ql='Query' token_dblabel="SQLite database" token_ql_shrt="Q" 106 <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=""> 107 token_user="True" token_mspuritydatalib="False" token_msp="False" token_help="">
103 <conditional name="@QL_SHRT@_dbPth_con"> 108 <conditional name="@QL_SHRT@_dbPth_con">
104 <param name="@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" > 109 <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> 110 <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> 111 <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> 112 <option value="msp" >MSP file (SQLite database will be created using using msp2db)</option>
108 </param> 113 </param>
109 <when value="userdb"> 114 <when value="userdb">
110 <param type="data" name="@QL_SHRT@_dbPth" label="@QL@ SQLite database" format="sqlite" help=""/> 115 <param type="data" name="@QL_SHRT@_dbPth" label="@QL@ SQLite database" format="sqlite" help=""/>
111 </when> 116 </when>
112 <when value="msp"> 117 <when value="msp">
113 <param type="data" name="@QL_SHRT@_msp" label="@QL@ MSP file" format="msp" help=""/> 118 <param type="data" name="@QL_SHRT@_msp" label="@QL@ MSP file" format="msp" help=""/>
114 </when> 119 </when>
115 120
116 <when value="msPurityData"> 121 <when value="msPurityData">
117 </when> 122 </when>
118 </conditional> 123 </conditional>
119 </xml> 124 </xml>
120 125
121 126
122 <xml name="filters" token_ql="Query" token_polarity_positive="false" token_ql_shrt="Q" 127 <xml name="filters" token_ql="Query" token_polarity_positive="false" token_ql_shrt="Q"
123 token_sources_select="false" token_instrument_types_select="false"> 128 token_sources_select="false" token_instrument_types_select="false">
124 129
125 <section name="@QL_SHRT@_filters" title="Filters" expanded="False"> 130 <section name="@QL_SHRT@_filters" title="Filters" expanded="False">
126 131
127 <param name="@QL_SHRT@_ppmPrec" type="float" value="5" label="ppm error of the precursor for spectra"/> 132 <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"/> 133 <param name="@QL_SHRT@_ppmProd" type="float" value="10" label="ppm error of the product for spectra"/>
129 134
130 <conditional name="@QL_SHRT@_raThres_cond"> 135 <conditional name="@QL_SHRT@_raThres_cond">
131 <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/> 136 <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/>
132 <when value="true"> 137 <when value="true">
133 <param name="@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/> 138 <param name="@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/>
134 </when> 139 </when>
135 <when value="false"> 140 <when value="false">
136 </when> 141 </when>
137 </conditional> 142 </conditional>
138 143
139 <conditional name="@QL_SHRT@_polarity_cond"> 144 <conditional name="@QL_SHRT@_polarity_cond">
140 <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" /> 145 <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" />
141 <when value="true"> 146 <when value="true">
142 <param name="@QL_SHRT@_polarity" type="select" label="Polarity" multiple="true" > 147 <param name="@QL_SHRT@_polarity" type="select" label="Polarity" multiple="true" >
143 <option value="positive" selected="@POLARITY_POSITIVE@">Positive</option> 148 <option value="positive" selected="@POLARITY_POSITIVE@">Positive</option>
146 </param> 151 </param>
147 </when> 152 </when>
148 <when value="false"> 153 <when value="false">
149 </when> 154 </when>
150 </conditional> 155 </conditional>
151 156
152 <conditional name="@QL_SHRT@_purity_cond"> 157 <conditional name="@QL_SHRT@_purity_cond">
153 <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/> 158 <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/>
154 <when value="true"> 159 <when value="true">
155 <param name="@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6" 160 <param name="@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6"
156 label="Precursor ion purity threshold"/> 161 label="Precursor ion purity threshold"/>
157 </when> 162 </when>
158 <when value="false"> 163 <when value="false">
159 </when> 164 </when>
160 </conditional> 165 </conditional>
161 166
162 <conditional name="@QL_SHRT@_xcmsGroups_cond"> 167 <conditional name="@QL_SHRT@_xcmsGroups_cond">
163 <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/> 168 <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/>
164 <when value="true"> 169 <when value="true">
165 <param name="@QL_SHRT@_xcmsGroups" type="text" value="" 170 <param name="@QL_SHRT@_xcmsGroups" type="text" value=""
166 label="XCMS group ids of spectra" 171 label="XCMS group ids of spectra"
167 help="comma seperated list of grpids (correspond to column 'grpid in c_peak_group')) 172 help="comma seperated list of grpids (correspond to column 'grpid in c_peak_group'))
168 e.g '12,27,30'" /> 173 e.g '12,27,30'" />
169 </when> 174 </when>
170 <when value="false"> 175 <when value="false">
171 </when> 176 </when>
172 </conditional> 177 </conditional>
173 178
174 179
175 <conditional name="@QL_SHRT@_pids_cond"> 180 <conditional name="@QL_SHRT@_pids_cond">
176 <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/> 181 <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/>
177 <when value="true"> 182 <when value="true">
178 <param name="@QL_SHRT@_pids" type="text" value="" 183 <param name="@QL_SHRT@_pids" type="text" value=""
179 label="pids of spectra (correspond to column 'pid; in s_peak_meta)" 184 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)) 185 help="comma seperated list of pids (correspond to column 'pid; in s_peak_meta))
181 e.g '3001,5561'" /> 186 e.g '3001,5561'" />
182 </when> 187 </when>
183 <when value="false"> 188 <when value="false">
184 </when> 189 </when>
185 </conditional> 190 </conditional>
186 191
187 192
188 <conditional name="@QL_SHRT@_rtrange_cond"> 193 <conditional name="@QL_SHRT@_rtrange_cond">
189 <param name="@QL_SHRT@_rtrange_bool" type="boolean" 194 <param name="@QL_SHRT@_rtrange_bool" type="boolean"
190 label="Filter on retention time range?" 195 label="Filter on retention time range?"
191 help="Filter the spectra between two points of retention time range"/> 196 help="Filter the spectra between two points of retention time range"/>
192 <when value="true"> 197 <when value="true">
193 <param name="@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)" 198 <param name="@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)"
194 type="float" value="0" help=""/> 199 type="float" value="0" help=""/>
196 type="float" value="3000" help=""/> 201 type="float" value="3000" help=""/>
197 </when> 202 </when>
198 <when value="false"> 203 <when value="false">
199 </when> 204 </when>
200 </conditional> 205 </conditional>
201 206
202 207
203 208
204 <conditional name="@QL_SHRT@_accessions_cond"> 209 <conditional name="@QL_SHRT@_accessions_cond">
205 <param name="@QL_SHRT@_accessions_bool" type="boolean" 210 <param name="@QL_SHRT@_accessions_bool" type="boolean"
206 label="Filter on accessions?" 211 label="Filter on accessions?"
207 help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/> 212 help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/>
208 <when value="true"> 213 <when value="true">
209 <param name="@QL_SHRT@_accessions" type="text" value="" 214 <param name="@QL_SHRT@_accessions" type="text" value=""
210 label="Spectra accessions" 215 label="Spectra accessions"
211 help="Comma seperated list of accessions)) 216 help="Comma seperated list of accessions))
212 e.g 'AC000001,BS001003,LIT00001'" /> 217 e.g 'AC000001,BS001003,LIT00001'" />
213 </when> 218 </when>
214 <when value="false"> 219 <when value="false">
215 </when> 220 </when>
216 </conditional> 221 </conditional>
217 222
218 223
219 <conditional name="@QL_SHRT@_sources_cond"> 224 <conditional name="@QL_SHRT@_sources_cond">
220 <param name="@QL_SHRT@_sources_bool" type="boolean" 225 <param name="@QL_SHRT@_sources_bool" type="boolean"
221 label="Filter on sources?" help="" value="@SOURCES_SELECT@" /> 226 label="Filter on sources?" help="" value="@SOURCES_SELECT@" />
222 <when value="true"> 227 <when value="true">
223 <param name="@QL_SHRT@_sources" type="select" multiple="true" 228 <param name="@QL_SHRT@_sources" type="select" multiple="true"
224 help="@QL_SHRT@ The default internal SQLite database of library (reference) spectra 229 help="@QL_SHRT@ The default internal SQLite database of library (reference) spectra
225 contains fragmentation spectra from MassBank, LipidBlast and GNPS. A copy is 230 contains fragmentation spectra from MassBank, LipidBlast and GNPS. A copy is
226 available from here: 231 available from here:
227 https://bioconductor.org/packages/release/data/experiment/html/msPurityData.html" > 232 https://bioconductor.org/packages/release/data/experiment/html/msPurityData.html" >
228 <option value="massbank" selected="true">MassBank from MoNa</option> 233 <option value="massbank" selected="true">MassBank from MoNa</option>
229 <option value="gnps" selected="true">GNPS</option> 234 <option value="gnps" selected="true">GNPS</option>
230 <option value="hmdb" selected="true">HMDB</option> 235 <option value="hmdb" selected="true">HMDB</option>
231 <option value="lipidblast" selected="true">LipidBlast</option> 236 <option value="lipidblast" selected="true">LipidBlast</option>
237 </when> 242 </when>
238 <when value="false"> 243 <when value="false">
239 </when> 244 </when>
240 </conditional> 245 </conditional>
241 <conditional name="@QL_SHRT@_instrumentTypes_cond"> 246 <conditional name="@QL_SHRT@_instrumentTypes_cond">
242 <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean" 247 <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean"
243 value="@INSTRUMENT_TYPES_SELECT@" 248 value="@INSTRUMENT_TYPES_SELECT@"
244 label="Filter on instrument type?" help="" /> 249 label="Filter on instrument type?" help="" />
245 <when value="true"> 250 <when value="true">
246 <param name="@QL_SHRT@_instrumentTypes" type="select" multiple="true" 251 <param name="@QL_SHRT@_instrumentTypes" type="select" multiple="true"
247 help="" > 252 help="" >
276 <option value="MALDI-TOF">MALDI-TOF</option> 281 <option value="MALDI-TOF">MALDI-TOF</option>
277 <option value="ALDI-TOFTOF">ALDI-TOFTOF</option> 282 <option value="ALDI-TOFTOF">ALDI-TOFTOF</option>
278 <option value="none">None</option> 283 <option value="none">None</option>
279 </param> 284 </param>
280 <param name="@QL_SHRT@_instrumentTypesUser" type="text" value="" 285 <param name="@QL_SHRT@_instrumentTypesUser" type="text" value=""
281 help="Types of the instruments to be included in the search. Use a comma to 286 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."/> 287 separate the instrument types or leave empty to ignore filter."/>
283 </when> 288 </when>
284 <when value="false"> 289 <when value="false">
285 </when> 290 </when>
286 </conditional> 291 </conditional>
287 <conditional name="@QL_SHRT@_instruments_cond"> 292 <conditional name="@QL_SHRT@_instruments_cond">
288 <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" /> 293 <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" />
289 <when value="true"> 294 <when value="true">
290 <param name="@QL_SHRT@_instruments" type="text" value="" 295 <param name="@QL_SHRT@_instruments" type="text" value=""
291 help="Known instrument names to filter on. Use a comma to 296 help="Known instrument names to filter on. Use a comma to
292 separate the instrument types or leave empty to ignore filter."/> 297 separate the instrument types or leave empty to ignore filter."/>
293 </when> 298 </when>
294 <when value="false"> 299 <when value="false">
295 </when> 300 </when>
296 </conditional> 301 </conditional>
297 302
298 303
299 304
300 <conditional name="@QL_SHRT@_spectraTypes_cond"> 305 <conditional name="@QL_SHRT@_spectraTypes_cond">
301 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?" 306 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
302 help="" /> 307 help="" />
303 <when value="true"> 308 <when value="true">
304 <param name="@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" > 309 <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> 310 <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
306 <option value="av_inter">Averaged inter spectra</option> 311 <option value="av_inter">Averaged inter spectra</option>
312 <when value="false"> 317 <when value="false">
313 </when> 318 </when>
314 </conditional> 319 </conditional>
315 320
316 <param name="@QL_SHRT@_spectraFilter" type="boolean" checked="true" 321 <param name="@QL_SHRT@_spectraFilter" type="boolean" checked="true"
317 label="Ignore any peaks flagged in the spectra in previous stages?" 322 label="Ignore any peaks flagged in the spectra in previous stages?"
318 help="" /> 323 help="" />
319 324
320 </section> 325 </section>
321 </xml> 326 </xml>
322 327
323 328
324 329
325 330
326 <xml name="citations"> 331 <xml name="citations">
327 <citations> 332 <citations>
328 <citation type="doi">10.1021/acs.analchem.6b04358</citation> 333 <citation type="doi">10.1021/acs.analchem.6b04358</citation>
329 <yield /> 334 <yield />