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comparison metfrag.xml @ 2:f151ee133612 draft default tip

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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"
author computational-metabolomics
date Tue, 14 Jul 2020 07:41:53 -0400
parents 9ee2e2ceb2c9
children
comparison
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1:9ee2e2ceb2c9 2:f151ee133612
1 <tool id="metfrag" name="MetFrag" version="2.4.5+galaxy2" profile="18.01"> 1 <tool id="metfrag" name="MetFrag" version="2.4.5+galaxy3" profile="18.01">
2 <description> 2 <description>
3 in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra 3 in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
49 49
50 --meta_select_col $meta_select_col 50 --meta_select_col $meta_select_col
51 --minMSMSpeaks $minMSMSpeaks 51 --minMSMSpeaks $minMSMSpeaks
52 --schema $schema 52 --schema $schema
53 53
54 $output_cl
55
54 $PreProcessFilter.UnconnectedCompoundFilter 56 $PreProcessFilter.UnconnectedCompoundFilter
55 $PreProcessFilter.IsotopeFilter 57 $PreProcessFilter.IsotopeFilter
56 58
57 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements' 59 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements'
58 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements' 60 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements'
59 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList' 61 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList'
60 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList' 62 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList'
61 --FilterIncludedElements '$PreProcessFilter.FilterIncludedElements' 63 --FilterIncludedElements '$PreProcessFilter.FilterIncludedElements'
62 --FilterExcludedElements '$PreProcessFilter.FilterExcludedElements' 64 --FilterExcludedElements '$PreProcessFilter.FilterExcludedElements'
63 --FilterIncludedExclusiveElements '$PreProcessFilter.FilterIncludedExclusiveElements' 65 --FilterIncludedExclusiveElements '$PreProcessFilter.FilterIncludedExclusiveElements'
66
67 #if $adducts_cond.adducts_selector == 'select':
68 #for $a in $adducts_cond.adducts
69 --adducts $a
70 #end for
71 #elif $adducts_cond.adducts_selector == 'all':
72 #if $polarity == 'pos':
73 --adducts [M+H]+
74 --adducts [M+NH4]+
75 --adducts [M+Na]+
76 --adducts [M+K]+
77 --adducts [M+CH3OH+H]+
78 --adducts [M+ACN+H]+
79 --adducts [M+ACN+Na]+
80 --adducts [M+2ACN+H]+
81 #elif $polarity == 'neg':
82 --adducts [M-H]-
83 --adducts [M+Cl]-
84 --adducts [M+HCOO]-
85 --adducts [M+CH3COO]-
86 #end if
87 #end if
64 88
65 $skip_invalid_adducts 89 $skip_invalid_adducts
66 --score_thrshld $PostProcessFilter.score_thrshld 90 --score_thrshld $PostProcessFilter.score_thrshld
67 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld 91 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld
68 92
99 <param argument="--polarity" type="select" label="Polarity" 123 <param argument="--polarity" type="select" label="Polarity"
100 help="The polarity used for the mode of acquisition"> 124 help="The polarity used for the mode of acquisition">
101 <option value="pos" selected="true">Positive</option> 125 <option value="pos" selected="true">Positive</option>
102 <option value="neg">Negative</option> 126 <option value="neg">Negative</option>
103 </param> 127 </param>
128
104 <param argument="--schema" type="select" label="Schema" 129 <param argument="--schema" type="select" label="Schema"
105 help="The schema used for the MSP file (auto will try automatically determine the schema)"> 130 help="The schema used for the MSP file (auto will try automatically determine the schema)">
106 <option value="auto" selected="True">Auto</option> 131 <option value="auto" selected="True">Auto</option>
107 <option value="msp">Generic MSP</option> 132 <option value="msp">Generic MSP</option>
108 <option value="massbank">MassBank</option> 133 <option value="massbank">MassBank</option>
109 </param> 134 </param>
110 <param argument="--meta_select_col" type="select" 135 <param argument="--meta_select_col" type="select"
111 label="Choose how additional metadata columns are extracted" 136 label="Choose how additional metadata columns are extracted"
112 help="The MetFrag output can have additional meta data columns added, these can be either extracted 137 help="The MetFrag output can have additional meta data columns added, these can be either extracted
113 from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns 138 from the MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns
114 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and : 139 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and :
115 e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns"> 140 e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns">
116 <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option> 141 <option value="name" >Extra metadata columns from the Name or RECORD_TITLE</option>
117 <option value="name_split">Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option> 142 <option value="name_split">Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option>
118 <option value="all">Extra metadata columns from all MSP parameters</option> 143 <option value="all" selected="true">Extra metadata columns from MSP parameters</option>
119 </param> 144 </param>
120 <conditional name="suspectlist"> 145 <conditional name="suspectlist">
121 <param name="suspectselector" type="select" label="Suspect list" 146 <param name="suspectselector" type="select" label="Suspect list"
122 help="Choose whether to include a suspect list"> 147 help="Choose whether to include a suspect list">
123 <option value="includesuspects" >Include suspect list</option> 148 <option value="includesuspects" >Include suspect list</option>
141 </when> 166 </when>
142 <when value="excludesuspects"> 167 <when value="excludesuspects">
143 <expand macro="metfrag_scoring" suspectlistscore="False" weights="1.0,1.0"/> 168 <expand macro="metfrag_scoring" suspectlistscore="False" weights="1.0,1.0"/>
144 </when> 169 </when>
145 </conditional> 170 </conditional>
146 <param argument="--minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/> 171
172 <conditional name="adducts_cond">
173 <param name="adducts_selector" type="select" label="How to handle adducts"
174 help="Choose whether to include a suspect list">
175 <option value="msp" selected="True">Use adducts defined in MSP file</option>
176 <option value="select" >Select from list</option>
177 <option value="all" >Use all available adducts for either pos or neg ionisation mode</option>
178 </param>
179 <when value="msp">
180 </when>
181 <when value="select">
182 <param argument="--adducts" label="Select adducts" type="select" help="" multiple="true" display="checkboxes">
183 <option value="[M+H]+" selected="True">[M+H]+ 1.007276</option>
184 <option value="[M+NH4]+">[M+NH4]+ 18.034374</option>
185 <option value="[M+Na]+">[M+Na]+ 22.989218</option>
186 <option value="[M+K]+">[M+K]+ 38.963158</option>
187 <option value="[M+CH3OH+H]+">[M+CH3OH+H]+ 33.033489</option>
188 <option value="[M+ACN+H]+">[M+ACN+H]+ 42.033823</option>
189 <option value="[M+ACN+Na]+">[M+ACN+Na]+ 64.015765</option>
190 <option value="[M+2ACN+H]+">[M+2ACN+H]+ 83.06037</option>
191 <option value="[M-H]-" >[M-H]- -1.007276</option>
192 <option value="[M+Cl]-">[M+Cl]- 34.969402</option>
193 <option value="[M+HCOO]-">[M+HCOO]- 44.99819</option>
194 <option value="[M+CH3COO]-">[M+CH3COO]- 59.01385</option>
195 </param>
196 </when>
197 <when value="all">
198 </when>
199 </conditional>
200
147 <param argument="--skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?" 201 <param argument="--skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?"
148 truevalue="--skip_invalid_adducts" falsevalue="" checked="true" 202 truevalue="--skip_invalid_adducts" falsevalue="" checked="true"
149 help="If no adduct type is provided within the MSP file or if the adduct type is not usable 203 help="If no adduct type is provided within the MSP file or if the adduct type is not usable
150 with MetFrag, set to 'yes' if these spectra should be skipped or 'no' if the default 204 with MetFrag, set to 'yes' if these spectra should be skipped or 'no' if the default
151 of [M+H]+ for pos data or [M-H]- for neg data should be used"/> 205 of [M+H]+ for pos data or [M-H]- for neg data should be used"/>
206
207 <param argument="minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/>
208 <param argument="--output_cl" type="boolean" checked="true"
209 truevalue="--output_cl" falsevalue=""
210 label="Output the MetFrag command line call" help="This will output all the parameters used
211 for each MetFrag command line call (including the fragment peaks)"/>
152 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False"> 212 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False">
153 <param argument="--UnconnectedCompoundFilter" type="boolean" checked="false" 213 <param argument="--UnconnectedCompoundFilter" type="boolean" checked="false"
154 truevalue="--UnconnectedCompoundFilter" falsevalue="" 214 truevalue="--UnconnectedCompoundFilter" falsevalue=""
155 label="filter non-connected compounds (e.g. salts)" help=""/> 215 label="filter non-connected compounds (e.g. salts)" help=""/>
156 <param argument="--IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter" 216 <param argument="--IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter"
211 <param name="schema" value="massbank"/> 271 <param name="schema" value="massbank"/>
212 <param name="skip_invalid_adducts" value="false"/> 272 <param name="skip_invalid_adducts" value="false"/>
213 <param name="MetFragDatabaseType" value="PubChem"/> 273 <param name="MetFragDatabaseType" value="PubChem"/>
214 <param name="MetFragDatabaseType" value="LocalCSV"/> 274 <param name="MetFragDatabaseType" value="LocalCSV"/>
215 <param name="LocalDatabasePath" value="demo_db.csv"/> 275 <param name="LocalDatabasePath" value="demo_db.csv"/>
276 <param name="meta_select_col" value="name"/>
277 <param name="output_cl" value="false"/>
216 <output name="results" file="metfrag_massbank.tabular"/> 278 <output name="results" file="metfrag_massbank.tabular"/>
217 </test> 279 </test>
218 <test> 280 <test>
219 <!-- Test "generic" style data format --> 281 <!-- Test "generic" style data format -->
220 <param name="input" value="generic_format.msp"/> 282 <param name="input" value="generic_format.msp"/>
222 <param name="MetFragDatabaseType" value="PubChem"/> 284 <param name="MetFragDatabaseType" value="PubChem"/>
223 <param name="skip_invalid_adducts" value="false"/> 285 <param name="skip_invalid_adducts" value="false"/>
224 <param name="MetFragDatabaseType" value="LocalCSV"/> 286 <param name="MetFragDatabaseType" value="LocalCSV"/>
225 <param name="LocalDatabasePath" value="demo_db.csv"/> 287 <param name="LocalDatabasePath" value="demo_db.csv"/>
226 <output name="results" file="metfrag_msp.tabular"/> 288 <output name="results" file="metfrag_msp.tabular"/>
289 <param name="meta_select_col" value="name"/>
290 <param name="output_cl" value="false"/>
227 </test> 291 </test>
228 <test> 292 <test>
229 <!-- Test PubChem API with "winter" dataset --> 293 <!-- Test PubChem API with "winter" dataset -->
230 <param name="input" value="winter_pos.msp"/> 294 <param name="input" value="winter_pos.msp"/>
231 <section name="PostProcessFilter"> 295 <section name="PostProcessFilter">
237 <test> 301 <test>
238 <!-- Test actual MassBank data for Glucose --> 302 <!-- Test actual MassBank data for Glucose -->
239 <param name="input" value="RP022611.txt"/> 303 <param name="input" value="RP022611.txt"/>
240 <param name="MetFragDatabaseType" value="LocalCSV"/> 304 <param name="MetFragDatabaseType" value="LocalCSV"/>
241 <param name="LocalDatabasePath" value="demo_db.csv"/> 305 <param name="LocalDatabasePath" value="demo_db.csv"/>
306 <param name="meta_select_col" value="name"/>
307 <param name="output_cl" value="false"/>
242 <output name="results" file="RP022611.tabular"/> 308 <output name="results" file="RP022611.tabular"/>
243 </test> 309 </test>
244 <test> 310 <test>
245 <!-- Test actual MassBank data for Glucose (all metadata columns in output--> 311 <!-- Test actual MassBank data for Glucose (all metadata columns in output-->
246 <param name="input" value="RP022611.txt"/> 312 <param name="input" value="RP022611.txt"/>
247 <param name="schema" value="massbank"/> 313 <param name="schema" value="massbank"/>
248 <param name="MetFragDatabaseType" value="LocalCSV"/> 314 <param name="MetFragDatabaseType" value="LocalCSV"/>
249 <param name="LocalDatabasePath" value="demo_db.csv"/> 315 <param name="LocalDatabasePath" value="demo_db.csv"/>
250 <param name="meta_select_col" value="all"/> 316 <param name="output_cl" value="false"/>
251 <output name="results" file="RP022611_all_col.tabular"/> 317 <output name="results" file="RP022611_all_col.tabular"/>
252 </test> 318 </test>
253 <test> 319 <test>
254 <!-- Test actual MassBank data for Glucose (include suspect list - default)--> 320 <!-- Test actual MassBank data for Glucose (include suspect list - default)-->
255 <param name="input" value="RP022611.txt"/> 321 <param name="input" value="RP022611.txt"/>
258 <param name="suspectselector" value="includesuspects"/> 324 <param name="suspectselector" value="includesuspects"/>
259 <conditional name="includesuspects_default_cond"> 325 <conditional name="includesuspects_default_cond">
260 <param name="includesuspects_default_bool" value="true"/> 326 <param name="includesuspects_default_bool" value="true"/>
261 </conditional> 327 </conditional>
262 </conditional> 328 </conditional>
329 <param name="meta_select_col" value="name"/>
330 <param name="output_cl" value="false"/>
263 <output name="results" file="RP022611_suspect_default.txt"/> 331 <output name="results" file="RP022611_suspect_default.txt"/>
264 </test> 332 </test>
265 <test> 333 <test>
266 <!-- Test invalid adduct --> 334 <!-- Test invalid adduct -->
267 <param name="input" value="invalid_adduct.msp"/> 335 <param name="input" value="invalid_adduct.msp"/>
268 <param name="skip_invalid_adducts" value="true"/> 336 <param name="skip_invalid_adducts" value="true"/>
337 <param name="meta_select_col" value="name"/>
338 <param name="output_cl" value="false"/>
269 <output name="results" file="invalid_adduct_result.txt" ftype="tabular"/> 339 <output name="results" file="invalid_adduct_result.txt" ftype="tabular"/>
340 </test>
341 <test>
342 <!-- Test all adducts-->
343 <param name="input" value="RP022611.txt"/>
344 <param name="schema" value="massbank"/>
345 <param name="polarity" value="neg"/>
346 <param name="skip_invalid_adducts" value="false"/>
347 <param name="MetFragDatabaseType" value="PubChem"/>
348 <param name="MetFragDatabaseType" value="LocalCSV"/>
349 <param name="LocalDatabasePath" value="demo_db.csv"/>
350 <param name="meta_select_col" value="name"/>
351 <param name="output_cl" value="false"/>
352 <output name="results" file="RP022611_all_adducts.tabular"/>
353 <conditional name="adducts_cond">
354 <param name="adducts_selector" value="all"/>
355 </conditional>
270 </test> 356 </test>
271 </tests> 357 </tests>
272 <help> 358 <help>
273 ------- 359 -------
274 MetFrag 360 MetFrag