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comparison spectralMatching.xml @ 15:945e73261fbb draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:30:07 +0000
parents 499c26566a7a
children
comparison
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14:499c26566a7a 15:945e73261fbb
1 <tool id="mspurity_spectralmatching" name="msPurity.spectralMatching" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@"> 1 <tool id="mspurity_spectralmatching" name="msPurity.spectralMatching" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description> 2 <description>
3 Perform spectral matching to MS/MS spectral libraries 3 Perform spectral matching to MS/MS spectral libraries
4 </description> 4 </description>
5
6 <macros> 5 <macros>
7 <import>macros.xml</import> 6 <import>macros.xml</import>
8 </macros> 7 </macros>
9 8 <expand macro="requirements"/>
10 <expand macro="requirements"> 9 <command detect_errors="exit_code"><![CDATA[
11 </expand> 10 Rscript '$__tool_directory__/spectralMatching.R'
12
13
14 <stdio>
15 <exit_code range="1:" />
16 </stdio>
17 <command interpreter="Rscript"><![CDATA[
18 spectralMatching.R
19 --outDir=. 11 --outDir=.
20 --cores=\${GALAXY_SLOTS:-4} 12 --cores=\${GALAXY_SLOTS:-4}
21 13
22 #if $Query.q_dbPth_con.q_dbPth_select == 'msPurityData' 14 #if $Query.q_dbPth_con.q_dbPth_select == 'msPurityData'
23 --q_defaultDb 15 --q_defaultDb
101 #end if 93 #end if
102 94
103 95
104 #if $Query.q_filters.q_sources_cond.q_sources_bool 96 #if $Query.q_filters.q_sources_cond.q_sources_bool
105 --q_sources=$Query.q_filters.q_sources_cond.q_sources 97 --q_sources=$Query.q_filters.q_sources_cond.q_sources
106 --q_sourcesUser="$Query.q_filters.q_sources_cond.q_sourcesUser" 98 --q_sourcesUser='$Query.q_filters.q_sources_cond.q_sourcesUser'
107 #end if 99 #end if
108 100
109 #if $Library.l_filters.l_sources_cond.l_sources_bool 101 #if $Library.l_filters.l_sources_cond.l_sources_bool
110 --l_sources=$Library.l_filters.l_sources_cond.l_sources 102 --l_sources=$Library.l_filters.l_sources_cond.l_sources
111 --l_sourcesUser="$Library.l_filters.l_sources_cond.l_sourcesUser" 103 --l_sourcesUser='$Library.l_filters.l_sources_cond.l_sourcesUser'
112 #end if 104 #end if
113 105
114 #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool 106 #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool
115 --q_instrumentTypes="$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes" 107 --q_instrumentTypes='$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes'
116 --q_instrumentTypesUser="$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser" 108 --q_instrumentTypesUser='$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser'
117 #end if 109 #end if
118 110
119 #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool 111 #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool
120 --l_instrumentTypes="$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes" 112 --l_instrumentTypes='$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes'
121 --l_instrumentTypesUser="$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser" 113 --l_instrumentTypesUser='$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser'
122 #end if 114 #end if
123 115
124 #if $Query.q_filters.q_instruments_cond.q_instruments_bool 116 #if $Query.q_filters.q_instruments_cond.q_instruments_bool
125 --q_instruments="$Query.q_filters.q_instruments_cond.q_instruments" 117 --q_instruments=$Query.q_filters.q_instruments_cond.q_instruments
126 #end if 118 #end if
127 119
128 #if $Library.l_filters.l_instruments_cond.l_instruments_bool 120 #if $Library.l_filters.l_instruments_cond.l_instruments_bool
129 --l_instruments="$Library.l_filters.l_instruments_cond.l_instruments" 121 --l_instruments='$Library.l_filters.l_instruments_cond.l_instruments'
130 #end if 122 #end if
131 123
132 #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool 124 #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool
133 --q_spectraTypes=$Query.q_filters.q_spectraTypes_cond.q_spectraTypes 125 --q_spectraTypes=$Query.q_filters.q_spectraTypes_cond.q_spectraTypes
134 #end if 126 #end if
161 153
162 #if $General.usePrecursors 154 #if $General.usePrecursors
163 --usePrecursors 155 --usePrecursors
164 #end if 156 #end if
165 157
166
167
168 ]]></command> 158 ]]></command>
169 <inputs> 159 <inputs>
170 160 <section name="Query" title="Query spectra input and filters" expanded="True">
171 161 <expand macro="sm_input" ql="Query" ql_shrt = "q" user="True" mspuritydatalib="False" msp="False"
172
173 <section name="Query" title="Query spectra input and filters" expanded="True">
174 <expand macro="sm_input" ql='Query' ql_shrt = "q" user="True" mspuritydatalib="False" msp="False"
175 help="Query SQLite database - in the standard XCMS msPurity workflow - the output 162 help="Query SQLite database - in the standard XCMS msPurity workflow - the output
176 of msPurity.createDatabase should be used here. However any SQLite database 163 of msPurity.createDatabase should be used here. However any SQLite database
177 following the schema of as https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/> 164 following the schema of as https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/>
178 <expand macro="filters" ql="Query" ql_shrt="q"/> 165 <expand macro="filters" ql="Query" ql_shrt="q"/>
179 </section> 166 </section>
180 167 <section name="Library" title="Library spectra input and filters" expanded="True">
181 <section name="Library" title="Library spectra input and filters" expanded="True"> 168 <expand macro="sm_input" ql="Library" ql_shrt = "l" user="False" mspuritydatalib="True" msp="False"
182 <expand macro="sm_input" ql='Library' ql_shrt = "l" user="False" mspuritydatalib="True" msp="False"
183 help="Library SQLite database - in the standard XCMS msPurity workflow - a default 169 help="Library SQLite database - in the standard XCMS msPurity workflow - a default
184 database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite 170 database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite
185 database following the schema of https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/> 171 database following the schema of https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/>
186 <expand macro="filters" ql="Library" ql_shrt="l"/> 172 <expand macro="filters" ql="Library" ql_shrt="l"/>
187 </section> 173 </section>
188 174 <section name="General" title="General arguments" expanded="False">
189 <section name="General" title="General arguments" expanded="False"> 175 <conditional name="rttol_cond">
190 <conditional name="rttol_cond">
191 <param name="rttol_bool" type="boolean" label="Filter on retention time match?" 176 <param name="rttol_bool" type="boolean" label="Filter on retention time match?"
192 help="" /> 177 help="" />
193 <when value="true"> 178 <when value="true">
194 <param name="rttol" type="float" value="30" min="0" 179 <param name="rttol" type="float" value="30" min="0"
195 label="Retention time tolerance (seconds)" 180 label="Retention time tolerance (seconds)"
196 help="Retention time tolerance in seconds to match precursors"/> 181 help="Retention time tolerance in seconds to match precursors"/>
197 </when> 182 </when>
198 <when value="false"> 183 <when value="false"/>
199 </when> 184 </conditional>
200 </conditional> 185 <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?"
201 186 help="If True, spectra will be filtered by similarity of precursors based on
202 187 the library and query ppm defined tolerance" />
203 <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?" 188 <param name="raW" label="Weighting for relative abundance" type="float" value="0.5"
204 help="If True, spectra will be filtered by similarity of precursors based on 189 help="Relative abundance weight for spectra (default to 0.5 as determined by
205 the library and query ppm defined tolerance" /> 190 massbank for ESI data)"/>
206 191 <param name="mzW" label="Weighting for mz" type="float" min="0" value="2"
207 <param name="raW" label="Weighting for relative abundance" 192 help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/>
208 type="float" value="0.5" 193 <conditional name="updateDb_cond">
209 help="Relative abundance weight for spectra (default to 0.5 as determined by
210 massbank for ESI data)"/>
211
212 <param name="mzW" label="Weighting for mz"
213 type="float" value="2"
214 help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/>
215
216 <conditional name="updateDb_cond">
217 <param name="updateDb" type="boolean" checked="true" 194 <param name="updateDb" type="boolean" checked="true"
218 label="Update database with results?" help="" /> 195 label="Update database with results?" help="" />
219 <when value="true"> 196 <when value="true">
220 <param name="copyDb" type="boolean" checked="true" 197 <param name="copyDb" type="boolean" checked="true"
221 label="Make a copy of the database?" 198 label="Make a copy of the database?"
222 help="A copy will be made of the input SQLite target database and the 199 help="A copy will be made of the input SQLite target database and the
223 results will be added to this copy. When False, the input SQLite 200 results will be added to this copy. When False, the input SQLite
224 database will be updated with the matching results. Use False if 201 database will be updated with the matching results. Use False if
225 you want to reduce storage space being used."/> 202 you want to reduce storage space being used."/>
226 </when> 203 </when>
227 <when value="false"> 204 <when value="false"/>
228 </when> 205 </conditional>
229 </conditional>
230
231
232
233 </section> 206 </section>
234
235
236
237
238 </inputs> 207 </inputs>
239 208
240 <outputs> 209 <outputs>
241 <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results" 210 <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results"
242 from_work_dir="db_with_spectral_matching.sqlite" > 211 from_work_dir="db_with_spectral_matching.sqlite" >
243 <filter>create_new_database is True</filter> 212 <filter>create_new_database is True</filter>
244 </data> 213 </data>
245 <data name="matches" format="tsv" label="${tool.name} on ${on_string}: matches" 214 <data name="matches" format="tsv" label="${tool.name} on ${on_string}: matches"
246 from_work_dir="matched_results.tsv" > 215 from_work_dir="matched_results.tsv" >
247 <filter>spectra_type_q == "scans"</filter> 216 <filter>spectra_type_q == "scans"</filter>
248 </data> 217 </data>
249 <data name="xcms_matches" format="tsv" label="${tool.name} on ${on_string}: XCMS matches" 218 <data name="xcms_matches" format="tsv" label="${tool.name} on ${on_string}: XCMS matches"
250 from_work_dir="xcms_matched_results.tsv" /> 219 from_work_dir="xcms_matched_results.tsv" />
251 </outputs> 220 </outputs>
252 <tests> 221 <tests>
253 <test> 222 <test>
254
255
256 <param name="q_dbPth" value="createDatabase_output.sqlite" /> 223 <param name="q_dbPth" value="createDatabase_output.sqlite" />
257 <param name="l_dbPth_select" value="userdb" /> 224 <param name="l_dbPth_select" value="userdb" />
258 <param name="l_dbPth" value="PR100037.sqlite" /> 225 <param name="l_dbPth" value="PR100037.sqlite" />
259
260 <param name="q_xcmsGroups_bool" value="true" /> 226 <param name="q_xcmsGroups_bool" value="true" />
261 <param name="l_accessions_bool" value="true" /> 227 <param name="l_accessions_bool" value="true" />
262 <param name="q_xcmsGroups" value="14" /> 228 <param name="q_xcmsGroups" value="14" />
263 <param name="l_accessions" value="PR100037" /> 229 <param name="l_accessions" value="PR100037" />
264 <output name="xcms_matches" file="spectralMatching_matched_results.tsv" /> 230 <output name="xcms_matches" file="spectralMatching_matched_results.tsv" />
266 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/> 232 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/>
267 </test> 233 </test>
268 <test> 234 <test>
269 <param name="l_instrumentTypes_bool" value="true" /> 235 <param name="l_instrumentTypes_bool" value="true" />
270 <param name="q_dbPth" value="createDatabase_output.sqlite" /> 236 <param name="q_dbPth" value="createDatabase_output.sqlite" />
271 <param name="l_dbPth_select" value="userdb" /> 237 <param name="l_dbPth_select" value="userdb" />
272 <param name="l_dbPth" value="PR100037.sqlite" /> 238 <param name="l_dbPth" value="PR100037.sqlite" />
273
274 <param name="q_xcmsGroups_bool" value="true" /> 239 <param name="q_xcmsGroups_bool" value="true" />
275 <param name="l_accessions_bool" value="true" /> 240 <param name="l_accessions_bool" value="true" />
276 <param name="q_xcmsGroups" value="14" /> 241 <param name="q_xcmsGroups" value="14" />
277 <param name="l_accessions" value="PR100037" /> 242 <param name="l_accessions" value="PR100037" />
278
279 <output name="xcms_matches" file="spectralMatching_matched_results_instrumentTypes.tsv" /> 243 <output name="xcms_matches" file="spectralMatching_matched_results_instrumentTypes.tsv" />
280 <output name="matches" file="spectralMatching_xcms_matched_results_instrumentTypes.tsv" /> 244 <output name="matches" file="spectralMatching_xcms_matched_results_instrumentTypes.tsv" />
281 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite" ftype="sqlite" compare="sim_size"/> 245 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite" ftype="sqlite" compare="sim_size"/>
282 </test> 246 </test>
283
284
285 </tests> 247 </tests>
286
287
288 248
289 <help><![CDATA[ 249 <help><![CDATA[
290 250
291 ============================================================= 251 =============================================================
292 Spectral matching 252 Spectral matching
405 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases 365 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases
406 .. _msPurity_spectral_matching_vignette: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html 366 .. _msPurity_spectral_matching_vignette: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
407 367
408 ]]></help> 368 ]]></help>
409 369
410 <expand macro="citations"> </expand> 370 <expand macro="citations"> </expand>
411 </tool> 371 </tool>