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comparison macros.xml @ 15:a2ba12977060 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 12:35:23 +0000
parents 64431b9affe2
children
comparison
equal deleted inserted replaced
14:64431b9affe2 15:a2ba12977060
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.11.4</token> 3 <token name="@TOOL_VERSION@">1.12.0</token>
4 <token name="@GALAXY_TOOL_VERSION@">0.2.7</token> 4 <token name="@GALAXY_TOOL_VERSION@">0</token>
5 5
6 <xml name="requirements"> 6 <xml name="requirements">
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement> 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>
9 <yield /> 15 <yield />
10 </requirements> 16 </requirements>
11 </xml> 17 </xml>
12 18
13 19
14 <xml name="offsets"> 20 <xml name="offsets">
15 <param name="minoffset" type="float" label="minoffset" value="0.5" argument='--minoffset' 21 <param argument="--minoffset" type="float" label="minoffset" value="0.5"
16 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is 22 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
17 100.0 then the range would be from 999.5 to 100.0"/> 23 100.0 then the range would be from 999.5 to 100.0"/>
18 <param name="maxoffset" type="float" label="maxoffset" value="0.5" argument='--maxoffset' 24 <param argument="--maxoffset" type="float" label="maxoffset" value="0.5"
19 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is 25 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is
20 100.0 then the range would be from 100.0 to 100.5"/> 26 100.0 then the range would be from 100.0 to 100.5"/>
21 </xml> 27 </xml>
22 <xml name="general_params"> 28 <xml name="general_params">
23 <param name="ilim" type="float" value="0.05" argument='--ilim' 29 <param argument="--ilim" type="float" value="0.05"
24 label="Threshold to remove peaks below x % of the relative intensity of 30 label="Threshold to remove peaks below x % of the relative intensity of
25 precursor of interest" 31 precursor of interest"
26 help="All peaks less than this percentage of the precursor ion of interest will be 32 help="All peaks less than this percentage of the precursor ion of interest will be
27 removed from the purity calculation, default is 5\% (0.05). 33 removed from the purity calculation, default is 5\% (0.05).
28 Essentially a noise filter to remove peaks that are thought to have either none or 34 Essentially a noise filter to remove peaks that are thought to have either none or
29 very limited impact on the resulting fragmentation spectra."/> 35 very limited impact on the resulting fragmentation spectra."/>
30 <param name="iw_norm" type="select" label="Normalisation for isolation efficiency"> 36 <param argument="--iw_norm" type="select" label="Normalisation for isolation efficiency">
31 <option value="gauss" >Gaussian</option> 37 <option value="gauss" >Gaussian</option>
32 <option value="rcosine" >Raised cosine</option> 38 <option value="rcosine" >Raised cosine</option>
33 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option> 39 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
34 <option value="none" selected="true" >No normalisation</option> 40 <option value="none" selected="true" >No normalisation</option>
35 </param> 41 </param>
36 <conditional name="isotopes"> 42 <conditional name="isotopes">
37 <param name="isotopes" type="select" label="Handling of isotopic peaks" > 43 <param argument="--isotopes" type="select" label="Handling of isotopic peaks" >
38 <option value="keep" >Keep isotopes in precursor ion purity calculation</option> 44 <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
39 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option> 45 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
40 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option> 46 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
41 </param> 47 </param>
42 <when value="keep"> 48 <when value="keep">
43 </when> 49 </when>
44 <when value="exclude_default"> 50 <when value="exclude_default">
45 </when> 51 </when>
46 <when value="user"> 52 <when value="user">
47 <param name="im" type="data" format="tabular" label="Isotope matrix" help=" 53 <param argument="--im" type="data" format="tabular" label="Isotope matrix" help="
48 tabular file composing of columns: 54 tabular file composing of columns:
49 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer', 55 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
50 'charge', 'relative atomic mass (int)', 'xflag']. 56 'charge', 'relative atomic mass (int)', 'xflag'].
51 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant. 57 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
52 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 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
56 </conditional> 62 </conditional>
57 </xml> 63 </xml>
58 64
59 65
60 <xml name="camera_xcms"> 66 <xml name="camera_xcms">
61 <param name="camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?" 67 <param argument="--camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?"
62 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called 68 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called
63 xa (or both). The XCMS object is nested within the CAMERA object so either can be used"> 69 xa (or both). The XCMS object is nested within the CAMERA object so either can be used">
64 <option value="xcms" selected="true" >XCMS (xset)</option> 70 <option value="xcms" selected="true" >XCMS (xset)</option>
65 <option value="camera" >CAMERA (xa)</option> 71 <option value="camera" >CAMERA (xa)</option>
66 </param> 72 </param>
93 <option value="no" selected="true">Use default grouped peaklist</option> 99 <option value="no" selected="true">Use default grouped peaklist</option>
94 </param> 100 </param>
95 <when value="no"> 101 <when value="no">
96 </when> 102 </when>
97 <when value="yes"> 103 <when value="yes">
98 <param type="data" name="grp_peaklist" label="grouped peaklist" 104 <param argument="--grp_peaklist" type="data" label="grouped peaklist"
99 help="User supplied grouped peaklist to add to the database (if additional columns required e.g. 105 help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
100 CAMERA annotations" format="tsv,tabular"/> 106 CAMERA annotations" format="tsv,tabular"/>
101 </when> 107 </when>
102 </conditional> 108 </conditional>
103 </xml> 109 </xml>
104
105 110
106 <xml name="sm_input" token_ql='Query' token_dblabel="SQLite database" token_ql_shrt="Q" 111 <xml name="sm_input" token_ql='Query' token_dblabel="SQLite database" token_ql_shrt="Q"
107 token_user="True" token_mspuritydatalib="False" token_msp="False" token_help=""> 112 token_user="True" token_mspuritydatalib="False" token_msp="False" token_help="">
108 <conditional name="@QL_SHRT@_dbPth_con"> 113 <conditional name="@QL_SHRT@_dbPth_con">
109 <param name="@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" > 114 <param argument="--@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" >
110 <option value="sqlite" selected="@USER@" >SQLite database of (LC)-MS/MS data</option> 115 <option value="sqlite" selected="@USER@" >SQLite database of (LC)-MS/MS data</option>
111 <option value="local_config" selected="@USER@" >Locally configured SQLite, MySQL or PostgreSQL database</option> 116 <option value="local_config" selected="@USER@" >Locally configured SQLite, MySQL or PostgreSQL database</option>
112 <option value="msPurityData" selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option> 117 <option value="msPurityData" selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option>
113 </param> 118 </param>
114 <when value="sqlite"> 119 <when value="sqlite">
115 <param type="data" name="@QL_SHRT@_dbPth" label="@QL@ SQLite database" format="sqlite" help=""/> 120 <param argument="--@QL_SHRT@_dbPth" type="data" label="@QL@ SQLite database" format="sqlite" help=""/>
116 </when> 121 </when>
117 <when value="local_config"> 122 <when value="local_config">
118 </when> 123 </when>
119 <when value="msPurityData"> 124 <when value="msPurityData">
120 </when> 125 </when>
125 <xml name="filters" token_ql="Query" token_polarity_positive="false" token_ql_shrt="Q" 130 <xml name="filters" token_ql="Query" token_polarity_positive="false" token_ql_shrt="Q"
126 token_sources_select="false" token_instrument_types_select="false"> 131 token_sources_select="false" token_instrument_types_select="false">
127 132
128 <section name="@QL_SHRT@_filters" title="Filters" expanded="False"> 133 <section name="@QL_SHRT@_filters" title="Filters" expanded="False">
129 134
130 <param name="@QL_SHRT@_ppmPrec" type="float" value="5" label="ppm error of the precursor for spectra"/> 135 <param argument="--@QL_SHRT@_ppmPrec" type="float" value="5" label="ppm error of the precursor for spectra"/>
131 <param name="@QL_SHRT@_ppmProd" type="float" value="10" label="ppm error of the product for spectra"/> 136 <param argument="--@QL_SHRT@_ppmProd" type="float" value="10" label="ppm error of the product for spectra"/>
132 137
133 <conditional name="@QL_SHRT@_raThres_cond"> 138 <conditional name="@QL_SHRT@_raThres_cond">
134 <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/> 139 <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/>
135 <when value="true"> 140 <when value="true">
136 <param name="@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/> 141 <param argument="--@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/>
137 </when> 142 </when>
138 <when value="false"> 143 <when value="false">
139 </when> 144 </when>
140 </conditional> 145 </conditional>
141 146
142 <conditional name="@QL_SHRT@_polarity_cond"> 147 <conditional name="@QL_SHRT@_polarity_cond">
143 <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" /> 148 <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" />
144 <when value="true"> 149 <when value="true">
145 <param name="@QL_SHRT@_polarity" type="select" label="Polarity" multiple="true" > 150 <param argument="--@QL_SHRT@_polarity" type="select" label="Polarity" multiple="true" >
146 <option value="positive" selected="@POLARITY_POSITIVE@">Positive</option> 151 <option value="positive" selected="@POLARITY_POSITIVE@">Positive</option>
147 <option value="negative" >Negative</option> 152 <option value="negative" >Negative</option>
148 <option value="NA" >NA</option> 153 <option value="NA" >NA</option>
149 </param> 154 </param>
150 </when> 155 </when>
153 </conditional> 158 </conditional>
154 159
155 <conditional name="@QL_SHRT@_purity_cond"> 160 <conditional name="@QL_SHRT@_purity_cond">
156 <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/> 161 <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/>
157 <when value="true"> 162 <when value="true">
158 <param name="@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6" 163 <param argument="--@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6"
159 label="Precursor ion purity threshold"/> 164 label="Precursor ion purity threshold"/>
160 </when> 165 </when>
161 <when value="false"> 166 <when value="false">
162 </when> 167 </when>
163 </conditional> 168 </conditional>
164 169
165 <conditional name="@QL_SHRT@_xcmsGroups_cond"> 170 <conditional name="@QL_SHRT@_xcmsGroups_cond">
166 <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/> 171 <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/>
167 <when value="true"> 172 <when value="true">
168 <param name="@QL_SHRT@_xcmsGroups" type="text" value="" 173 <param argument="--@QL_SHRT@_xcmsGroups" type="text" value=""
169 label="XCMS group ids of spectra" 174 label="XCMS group ids of spectra"
170 help="comma seperated list of grpids (correspond to column 'grpid in c_peak_group')) 175 help="comma seperated list of grpids (correspond to column 'grpid in c_peak_group'))
171 e.g '12,27,30'" /> 176 e.g '12,27,30'" />
172 </when> 177 </when>
173 <when value="false"> 178 <when value="false">
176 181
177 182
178 <conditional name="@QL_SHRT@_pids_cond"> 183 <conditional name="@QL_SHRT@_pids_cond">
179 <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/> 184 <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/>
180 <when value="true"> 185 <when value="true">
181 <param name="@QL_SHRT@_pids" type="text" value="" 186 <param argument="--@QL_SHRT@_pids" type="text" value=""
182 label="pids of spectra (correspond to column 'pid; in s_peak_meta)" 187 label="pids of spectra (correspond to column 'pid; in s_peak_meta)"
183 help="comma seperated list of pids (correspond to column 'pid; in s_peak_meta)) 188 help="comma seperated list of pids (correspond to column 'pid; in s_peak_meta))
184 e.g '3001,5561'" /> 189 e.g '3001,5561'" />
185 </when> 190 </when>
186 <when value="false"> 191 <when value="false">
191 <conditional name="@QL_SHRT@_rtrange_cond"> 196 <conditional name="@QL_SHRT@_rtrange_cond">
192 <param name="@QL_SHRT@_rtrange_bool" type="boolean" 197 <param name="@QL_SHRT@_rtrange_bool" type="boolean"
193 label="Filter on retention time range?" 198 label="Filter on retention time range?"
194 help="Filter the spectra between two points of retention time range"/> 199 help="Filter the spectra between two points of retention time range"/>
195 <when value="true"> 200 <when value="true">
196 <param name="@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)" 201 <param argument="--@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)"
197 type="float" value="0" help=""/> 202 type="float" value="0" help=""/>
198 <param name="@QL_SHRT@_rtrangeMax" label="Maximum retention time range (seconds)" 203 <param argument="--@QL_SHRT@_rtrangeMax" label="Maximum retention time range (seconds)"
199 type="float" value="3000" help=""/> 204 type="float" value="3000" help=""/>
200 </when> 205 </when>
201 <when value="false"> 206 <when value="false">
202 </when> 207 </when>
203 </conditional> 208 </conditional>
207 <conditional name="@QL_SHRT@_accessions_cond"> 212 <conditional name="@QL_SHRT@_accessions_cond">
208 <param name="@QL_SHRT@_accessions_bool" type="boolean" 213 <param name="@QL_SHRT@_accessions_bool" type="boolean"
209 label="Filter on accessions?" 214 label="Filter on accessions?"
210 help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/> 215 help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/>
211 <when value="true"> 216 <when value="true">
212 <param name="@QL_SHRT@_accessions" type="text" value="" 217 <param argument="--@QL_SHRT@_accessions" type="text" value=""
213 label="Spectra accessions" 218 label="Spectra accessions"
214 help="Comma seperated list of accessions)) 219 help="Comma seperated list of accessions))
215 e.g 'AC000001,BS001003,LIT00001'" /> 220 e.g 'AC000001,BS001003,LIT00001'" />
216 </when> 221 </when>
217 <when value="false"> 222 <when value="false">
221 226
222 <conditional name="@QL_SHRT@_sources_cond"> 227 <conditional name="@QL_SHRT@_sources_cond">
223 <param name="@QL_SHRT@_sources_bool" type="boolean" 228 <param name="@QL_SHRT@_sources_bool" type="boolean"
224 label="Filter on sources?" help="" value="@SOURCES_SELECT@" /> 229 label="Filter on sources?" help="" value="@SOURCES_SELECT@" />
225 <when value="true"> 230 <when value="true">
226 <param name="@QL_SHRT@_sources" type="select" multiple="true" 231 <param argument="--@QL_SHRT@_sources" type="select" multiple="true"
227 help="@QL_SHRT@ The default internal SQLite database of library (reference) spectra 232 help="@QL_SHRT@ The default internal SQLite database of library (reference) spectra
228 contains fragmentation spectra from MassBank, LipidBlast and GNPS. A copy is 233 contains fragmentation spectra from MassBank, LipidBlast and GNPS. A copy is
229 available from here: 234 available from here:
230 https://bioconductor.org/packages/release/data/experiment/html/msPurityData.html" > 235 https://bioconductor.org/packages/release/data/experiment/html/msPurityData.html" >
231 <option value="massbank" selected="true">MassBank from MoNa</option> 236 <option value="massbank" selected="true">MassBank from MoNa</option>
244 <conditional name="@QL_SHRT@_instrumentTypes_cond"> 249 <conditional name="@QL_SHRT@_instrumentTypes_cond">
245 <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean" 250 <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean"
246 value="@INSTRUMENT_TYPES_SELECT@" 251 value="@INSTRUMENT_TYPES_SELECT@"
247 label="Filter on instrument type?" help="" /> 252 label="Filter on instrument type?" help="" />
248 <when value="true"> 253 <when value="true">
249 <param name="@QL_SHRT@_instrumentTypes" type="select" multiple="true" 254 <param argument="--@QL_SHRT@_instrumentTypes" type="select" multiple="true"
250 help="" > 255 help="" >
251 <option value="APCI-ITFT" selected="true" >APCI-ITFT</option> 256 <option value="APCI-ITFT" selected="true" >APCI-ITFT</option>
252 <option value="APCI-ITTOF" selected="true" >APCI-ITTOF</option> 257 <option value="APCI-ITTOF" selected="true" >APCI-ITTOF</option>
253 <option value="CE-ESI-TOF" selected="true" >CE-ESI-TOF</option> 258 <option value="CE-ESI-TOF" selected="true" >CE-ESI-TOF</option>
254 <option value="CI-B">CI-B</option> 259 <option value="CI-B">CI-B</option>
301 <option value="QqQ" selected="true">QqQ</option> 306 <option value="QqQ" selected="true">QqQ</option>
302 <option value="Q-TOF" selected="true">Q-TOF</option> 307 <option value="Q-TOF" selected="true">Q-TOF</option>
303 <option value="Quattro_QQQ" selected="true">Quattro_QQQ</option> 308 <option value="Quattro_QQQ" selected="true">Quattro_QQQ</option>
304 <option value="none">None</option> 309 <option value="none">None</option>
305 </param> 310 </param>
306 <param name="@QL_SHRT@_instrumentTypesUser" type="text" value="" 311 <param argument="--@QL_SHRT@_instrumentTypesUser" type="text" value=""
307 help="Types of the instruments to be included in the search. Use a comma to 312 help="Types of the instruments to be included in the search. Use a comma to
308 separate the instrument types or leave empty to ignore filter."/> 313 separate the instrument types or leave empty to ignore filter."/>
309 </when> 314 </when>
310 <when value="false"> 315 <when value="false">
311 </when> 316 </when>
312 </conditional> 317 </conditional>
313 <conditional name="@QL_SHRT@_instruments_cond"> 318 <conditional name="@QL_SHRT@_instruments_cond">
314 <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" /> 319 <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" />
315 <when value="true"> 320 <when value="true">
316 <param name="@QL_SHRT@_instruments" type="text" value="" 321 <param argument="--@QL_SHRT@_instruments" type="text" value=""
317 help="Known instrument names to filter on. Use a comma to 322 help="Known instrument names to filter on. Use a comma to
318 separate the instrument types or leave empty to ignore filter."/> 323 separate the instrument types or leave empty to ignore filter."/>
319 </when> 324 </when>
320 <when value="false"> 325 <when value="false">
321 </when> 326 </when>
325 330
326 <conditional name="@QL_SHRT@_spectraTypes_cond"> 331 <conditional name="@QL_SHRT@_spectraTypes_cond">
327 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?" 332 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
328 help="" /> 333 help="" />
329 <when value="true"> 334 <when value="true">
330 <param name="@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" > 335 <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" >
331 <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option> 336 <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
332 <option value="av_inter">Averaged inter spectra</option> 337 <option value="av_inter">Averaged inter spectra</option>
333 <option value="av_intra">Averaged intra spectra </option> 338 <option value="av_intra">Averaged intra spectra </option>
334 <option value="scans">All individual scans</option> 339 <option value="scans">All individual scans</option>
335 <option value="NA">Not applicable/defined</option> 340 <option value="NA">Not applicable/defined</option>
337 </when> 342 </when>
338 <when value="false"> 343 <when value="false">
339 </when> 344 </when>
340 </conditional> 345 </conditional>
341 346
342 <param name="@QL_SHRT@_spectraFilter" type="boolean" checked="true" 347 <param argument="--@QL_SHRT@_spectraFilter" type="boolean" checked="true"
343 label="Ignore any peaks flagged in the spectra in previous stages?" 348 label="Ignore any peaks flagged in the spectra in previous stages?"
344 help="" /> 349 help="" />
345 350
346 </section> 351 </section>
347 </xml> 352 </xml>