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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
author tomnl
date Fri, 04 Oct 2019 07:15:52 -0400
parents 9a3019c609d9
children
comparison
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8:9a3019c609d9 9:5763234618d4
1 <tool id="metfrag" name="MetFrag" version="2.4.5+galaxy0.1.13"> 1 <tool id="metfrag" name="MetFrag" version="2.4.5+galaxy1">
2 <description> </description> 2 <description>
3 in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
3 <requirements> 8 <requirements>
4 <requirement type="package" version="2.4.5">metfrag</requirement> 9 <requirement type="package" version="2.4.5">metfrag</requirement>
5 </requirements> 10 </requirements>
6 <stdio> 11 <stdio>
7 <regex match="Cannot allocate memory" 12 <regex match="Cannot allocate memory"
9 level="fatal_oom" 14 level="fatal_oom"
10 description="Out of memory error occurred" /> 15 description="Out of memory error occurred" />
11 </stdio> 16 </stdio>
12 <command detect_errors="exit_code"> 17 <command detect_errors="exit_code">
13 <![CDATA[ 18 <![CDATA[
14 19 python '$__tool_directory__/metfrag.py'
15 python $__tool_directory__/metfrag.py 20 --input_pth '$input'
16 --input_pth "$input"
17 --result_pth '$results' 21 --result_pth '$results'
18 --temp_dir './temp/' 22 --temp_dir './temp/'
19 23
20 --cores_top_level \${GALAXY_SLOTS:-4} 24 --cores_top_level \${GALAXY_SLOTS:-4}
21 25
22 --MetFragDatabaseType '$db_select.MetFragDatabaseType' 26 --MetFragDatabaseType '$db_select.MetFragDatabaseType'
23 27
24 #if $db_select.MetFragDatabaseType == "LocalCSV": 28 #if $db_select.MetFragDatabaseType == 'LocalCSV':
25 --LocalDatabasePath '$db_select.LocalDatabasePath' 29 --LocalDatabasePath '$db_select.LocalDatabasePath'
26 #elif $db_select.MetFragDatabaseType == "MetChem": 30 #elif $db_select.MetFragDatabaseType == 'MetChem':
27 --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp' 31 --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp'
28 #end if 32 #end if
29 33
30 --DatabaseSearchRelativeMassDeviation $DatabaseSearchRelativeMassDeviation 34 --DatabaseSearchRelativeMassDeviation $DatabaseSearchRelativeMassDeviation
31 --FragmentPeakMatchRelativeMassDeviation $FragmentPeakMatchRelativeMassDeviation 35 --FragmentPeakMatchRelativeMassDeviation $FragmentPeakMatchRelativeMassDeviation
35 --MetFragScoreTypes '$suspectlist.MetFragScoreTypes' 39 --MetFragScoreTypes '$suspectlist.MetFragScoreTypes'
36 --MetFragScoreWeights '$suspectlist.MetFragScoreWeights' 40 --MetFragScoreWeights '$suspectlist.MetFragScoreWeights'
37 41
38 #if $suspectlist.suspectselector == 'includesuspects': 42 #if $suspectlist.suspectselector == 'includesuspects':
39 #if $suspectlist.includesuspects_default_cond: 43 #if $suspectlist.includesuspects_default_cond:
40 --ScoreSuspectLists '$__tool_directory__/test-data/UNPD_DB.inchikeys.txt' 44 --ScoreSuspectLists '$__tool_directory__/UNPD_DB.inchikeys.txt'
41 #else 45 #else
42 --ScoreSuspectLists '$suspectlist.includesuspects_custom_cond.ScoreSuspectLists' 46 --ScoreSuspectLists '$suspectlist.includesuspects_custom_cond.ScoreSuspectLists'
43 #end if 47 #end if
44 #end if 48 #end if
45 49
47 --minMSMSpeaks $minMSMSpeaks 51 --minMSMSpeaks $minMSMSpeaks
48 --schema $schema 52 --schema $schema
49 53
50 $PreProcessFilter.UnconnectedCompoundFilter 54 $PreProcessFilter.UnconnectedCompoundFilter
51 $PreProcessFilter.IsotopeFilter 55 $PreProcessFilter.IsotopeFilter
52
53 56
54 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements' 57 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements'
55 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements' 58 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements'
56 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList' 59 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList'
57 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList' 60 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList'
61 64
62 $skip_invalid_adducts 65 $skip_invalid_adducts
63 --score_thrshld $PostProcessFilter.score_thrshld 66 --score_thrshld $PostProcessFilter.score_thrshld
64 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld 67 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld
65 68
66
67
68
69
70 ]]></command> 69 ]]></command>
71 <inputs> 70 <inputs>
72 71 <param name="input" type="data" format="msp" label="MSP file (Output from Create MSP tool)"/>
73 <param name="input" type="data" format="msp,txt" label="MSP file (Output from Create MSP tool)"/>
74 <conditional name="db_select"> 72 <conditional name="db_select">
75 <param name="MetFragDatabaseType" type="select" label="Choose Compound Database" 73 <param argument="--MetFragDatabaseType" type="select" label="Choose Compound Database">
76 argument="--MetFragDatabaseType">
77 <option value="PubChem" selected="true">PubChem</option> 74 <option value="PubChem" selected="true">PubChem</option>
78 <option value="KEGG">KEGG</option> 75 <option value="KEGG">KEGG</option>
79 <option value="LocalCSV">Local database (csv)</option> 76 <option value="LocalCSV">Local database (csv)</option>
80 <option value="MetChem">MetChem</option> 77 <option value="MetChem">MetChem</option>
81 </param> 78 </param>
82 <when value="MetChem"> 79 <when value="MetChem">
83 <param name="LocalMetChemDatabaseServerIp" type="text" label="MetChem URL" 80 <param argument="--LocalMetChemDatabaseServerIp" type="text" label="MetChem URL"/>
84 argument="--LocalMetChemDatabaseServerIp" />
85 </when> 81 </when>
86 <when value="LocalCSV"> 82 <when value="LocalCSV">
87 <param name="LocalDatabasePath" type="data" format="csv" label="Local database of compounds (CSV format)" argument="--LocalDatabasePath"/> 83 <param argument="--LocalDatabasePath" type="data" format="csv"
84 label="Local database of compounds (CSV format)" />
88 </when> 85 </when>
89 <when value="KEGG"> 86 <when value="KEGG"/>
90 </when> 87 <when value="PubChem"/>
91 <when value="PubChem">
92 </when>
93 </conditional> 88 </conditional>
94 <param name="DatabaseSearchRelativeMassDeviation" type="float" value="10" 89 <param argument="--DatabaseSearchRelativeMassDeviation" type="float" min="0" value="10"
95 label="Relative Mass Deviation for database search (ppm)" argument="--DatabaseSearchRelativeMassDeviation" 90 label="Relative Mass Deviation for database search (ppm)"
96 help="A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses"/> 91 help="A value in ppm that defines the deviation of theoretical masses in the database
97 <param name="FragmentPeakMatchRelativeMassDeviation" type="float" value="5" 92 vs. the measured masses"/>
98 label="Fragment Peak Match Relative Mass Deviation (ppm)" argument="--FragmentPeakMatchRelativeMassDeviation" 93 <param argument="--FragmentPeakMatchRelativeMassDeviation" type="float" min="0" value="5"
94 label="Fragment Peak Match Relative Mass Deviation (ppm)"
99 help="Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks" /> 95 help="Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks" />
100 <param name="FragmentPeakMatchAbsoluteMassDeviation" type="float" value="0.001" 96 <param argument="--FragmentPeakMatchAbsoluteMassDeviation" type="float" min="0" value="0.001"
101 label="Fragment Peak Match Absolute Mass Deviation (Da)" argument="FragmentPeakMatchAbsoluteMassDeviation" 97 label="Fragment Peak Match Absolute Mass Deviation (Da)"
102 help="Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks" /> 98 help="Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks" />
103 <param name="polarity" type="select" label="Polarity" help="The polarity used for the mode of acquisition"> 99 <param argument="--polarity" type="select" label="Polarity"
100 help="The polarity used for the mode of acquisition">
104 <option value="pos" selected="true">Positive</option> 101 <option value="pos" selected="true">Positive</option>
105 <option value="neg">Negative</option> 102 <option value="neg">Negative</option>
106 </param> 103 </param>
107 <param name="schema" type="select" label="Schema" 104 <param argument="--schema" type="select" label="Schema"
108 help="The schema used for the MSP file (auto will try automatically determine the schema)"> 105 help="The schema used for the MSP file (auto will try automatically determine the schema)">
109 <option value="auto" selected="True">Auto</option> 106 <option value="auto" selected="True">Auto</option>
110 <option value="msp" >Generic MSP</option> 107 <option value="msp">Generic MSP</option>
111 <option value="massbank">MassBank</option> 108 <option value="massbank">MassBank</option>
112 </param> 109 </param>
113 <param name="meta_select_col" type="select" label="Choose how additional metadata columns are extracted" 110 <param argument="--meta_select_col" type="select"
111 label="Choose how additional metadata columns are extracted"
114 help="The MetFrag output can have additional meta data columns added, these can be either extracted 112 help="The MetFrag output can have additional meta data columns added, these can be either extracted
115 from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns 113 from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns
116 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and : 114 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and :
117 e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns"> 115 e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns">
118 <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option> 116 <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option>
119 <option value="name_split" >Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option> 117 <option value="name_split">Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option>
120 <option value="all">Extra metadata columns from all MSP parameters</option> 118 <option value="all">Extra metadata columns from all MSP parameters</option>
121 </param> 119 </param>
122
123 <conditional name="suspectlist"> 120 <conditional name="suspectlist">
124 <param name="suspectselector" type="select" optional="False" label="Suspect list" help="Choose whether to include a suspect list"> 121 <param name="suspectselector" type="select" label="Suspect list"
122 help="Choose whether to include a suspect list">
125 <option value="includesuspects" >Include suspect list</option> 123 <option value="includesuspects" >Include suspect list</option>
126 <option value="excludesuspects" selected="True">Do not include suspect list</option> 124 <option value="excludesuspects" selected="True">Do not include suspect list</option>
127 </param> 125 </param>
128 <when value="includesuspects"> 126 <when value="includesuspects">
129 <conditional name="includesuspects_default_cond"> 127 <conditional name="includesuspects_default_cond">
130 <param name="includesuspects_default_bool" type="boolean" label="Use default list of suspect compounds?" 128 <param name="includesuspects_default_bool" type="boolean"
129 label="Use default list of suspect compounds?"
131 help="Either provide a file containing a list of suspect compounds or a default file 130 help="Either provide a file containing a list of suspect compounds or a default file
132 of of an aggregated list of in silico predicted MS/MS spectra of natural products 131 of an aggregated list of in silico predicted MS/MS spectra of natural products
133 from the Universal Natural Products Database (http://pkuxxj.pku.edu.cn/UNPD/index.php). 132 from the Universal Natural Products Database (http://pkuxxj.pku.edu.cn/UNPD/index.php).
134 The list is an aggregated version of the github repository https://github.com/oolonek/ISDB/tree/master/Data/dbs."/> 133 The list is an aggregated version of the github repository https://github.com/oolonek/ISDB/tree/master/Data/dbs."/>
135 <when value="true"> 134 <when value="true"/>
136 </when>
137 <when value="false"> 135 <when value="false">
138 <param name="ScoreSuspectLists" type="data" format="txt" optional="False" label="Suspect list file" 136 <param argument="--ScoreSuspectLists" type="data" format="txt" optional="True"
139 help="File containing a list of suspects inchikeys" /> 137 label="Suspect list file" help="File containing a list of suspects inchikeys" />
140 </when> 138 </when>
141 </conditional> 139 </conditional>
142 140 <expand macro="metfrag_scoring"/>
143 <param name="MetFragScoreTypes" type="text" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore" optional="False" label="MetFrag Score Types" help="The type of scores MetFrag is calculating. Please do not change the value unless you know what you are doing." />
144 <param name="MetFragScoreWeights" type="text" value="0.4,0.6,1.0" optional="False" label="MetFrag Score Weights" help="The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100 percent." />
145 </when> 141 </when>
146 <when value="excludesuspects"> 142 <when value="excludesuspects">
147 <param name="MetFragScoreTypes" type="text" value="FragmenterScore,OfflineMetFusionScore" optional="False" label="MetFrag Score Types" help="The type of scores MetFrag is calculating. Please do not change the value unless you know what you are doing." /> 143 <expand macro="metfrag_scoring" suspectlistscore="False" weights="1.0,1.0"/>
148 <param name="MetFragScoreWeights" type="text" value="1.0,1.0" optional="False" label="MetFrag Score Weights" help="The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100 percent." />
149 </when> 144 </when>
150 </conditional> 145 </conditional>
151 146 <param argument="--minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/>
152 <param name="minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/> 147 <param argument="--skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?"
153 <param name="skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?"
154 truevalue="--skip_invalid_adducts" falsevalue="" checked="true" 148 truevalue="--skip_invalid_adducts" falsevalue="" checked="true"
155 help="If no adduct type is provided within the MSP file or if the adduct type is not usable 149 help="If no adduct type is provided within the MSP file or if the adduct type is not usable
156 with MetFrag, set to 'yes' if these spectra should be skipped or 'no' if the default 150 with MetFrag, set to 'yes' if these spectra should be skipped or 'no' if the default
157 of [M+H]+ for pos data or [M-H]- for neg data should be used"/> 151 of [M+H]+ for pos data or [M-H]- for neg data should be used"/>
158 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False"> 152 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False">
159 <param name="UnconnectedCompoundFilter" type="boolean" checked="false" truevalue="--UnconnectedCompoundFilter" 153 <param argument="--UnconnectedCompoundFilter" type="boolean" checked="false"
160 falsevalue="" label="filter non-connected compounds (e.g. salts)" help=""/> 154 truevalue="--UnconnectedCompoundFilter" falsevalue=""
161 <param name="IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter" falsevalue="" 155 label="filter non-connected compounds (e.g. salts)" help=""/>
162 label="filter compounds containing non-standard isotopes" help=""/> 156 <param argument="--IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter"
163 <param name="FilterMinimumElements" type="text" label="Minimum Elements Filter" 157 falsevalue="" label="filter compounds containing non-standard isotopes" help=""/>
164 help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least 2 nitrogens and 3 oxygens"/> 158 <param argument="--FilterMinimumElements" type="text"
165 <param name="FilterMaximumElements" type="text" label="Maximum Elements Filter" 159 optional="true" label="Minimum Elements Filter"
166 help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at maximum 5 nitrogens and 7 oxygens"/> 160 help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least
167 <param name="FilterSmartsInclusionList" type="text" label="Include substructures" 161 2 nitrogens and 3 oxygens">
168 help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds containing benzene"/> 162 <expand macro="text-alphanumeric-regex-validator"/>
169 <param name="FilterSmartsExclusionList" type="text" label="Exclude substructures" 163 </param>
170 help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds containing hydroxyl groups"/> 164 <param argument="--FilterMaximumElements" type="text"
171 <param name="FilterIncludedElements" type="text" label="Include elements" 165 optional="true" label="Maximum Elements Filter"
172 help="Filter by presence of defined elements (other elements are allowed). Ex: 'N,O' include compounds containing nitrogen and oxygen" /> 166 help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at
173 <param name="FilterIncludedExclusiveElements" type="text" label="Include elements (exclusive)" 167 maximum 5 nitrogens and 7 oxygens">
174 help="Filter by presence of defined elements (no other elements are allowed). Ex: 'N,O' include compounds only composed of nitrogen and oxygen" /> 168 <expand macro="text-alphanumeric-regex-validator"/>
175 <param name="FilterExcludedElements" type="text" label="Exclude elements" 169 </param>
176 help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out compounds including bromine or chlorine"/> 170 <param argument="--FilterSmartsInclusionList" type="text"
171 optional="true" label="Include substructures"
172 help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds
173 containing benzene"/>
174 <param argument="--FilterSmartsExclusionList" type="text"
175 optional="true" label="Exclude substructures"
176 help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds
177 containing hydroxyl groups"/>
178 <param argument="--FilterIncludedElements" type="text"
179 optional="true" label="Include elements"
180 help="Filter by presence of defined elements (other elements are allowed).
181 Ex: 'N,O' include compounds containing nitrogen and oxygen" >
182 <expand macro="text-alphanumeric-comma-regex-validator"/>
183 </param>
184 <param argument="--FilterIncludedExclusiveElements" type="text"
185 optional="true" label="Include elements (exclusive)"
186 help="Filter by presence of defined elements (no other elements are allowed).
187 Ex: 'N,O' include compounds only composed of nitrogen and oxygen" >
188 <expand macro="text-alphanumeric-comma-regex-validator"/>
189 </param>
190 <param argument="--FilterExcludedElements" type="text"
191 optional="true" label="Exclude elements"
192 help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out
193 compounds including bromine or chlorine">
194 <expand macro="text-alphanumeric-comma-regex-validator"/>
195 </param>
177 </section> 196 </section>
178
179 <section name="PostProcessFilter" title="PostProcessing filters" expanded="False"> 197 <section name="PostProcessFilter" title="PostProcessing filters" expanded="False">
180 <param name="score_thrshld" type="float" label="Threshold for score after MetFrag search" max="1" min="0" value="0"/> 198 <param argument="--score_thrshld" type="float" label="Threshold for score after MetFrag search"
181 <param name="pctexplpeak_thrshld" type="float" label="Minimum percentage of explain peaks" max="100" min="0" value="0"/> 199 max="1" min="0" value="0"/>
200 <param argument="--pctexplpeak_thrshld" type="float" label="Minimum percentage of explain peaks"
201 max="100" min="0" value="0"/>
182 </section> 202 </section>
183
184 </inputs> 203 </inputs>
185 <outputs> 204 <outputs>
186 <data name="results" format="tabular" label="${tool.name} results of ${input.name}" /> 205 <data name="results" format="tabular"/>
187 </outputs> 206 </outputs>
188 <tests> 207 <tests>
189 <test> 208 <test>
190 <!-- Test "massbank" style data format --> 209 <!-- Test "massbank" style data format -->
191 <param name="input" value="massbank_format.txt"/> 210 <param name="input" value="massbank_format.txt"/>
192 <param name="schema" value="massbank"/> 211 <param name="schema" value="massbank"/>
212 <param name="skip_invalid_adducts" value="false"/>
213 <param name="MetFragDatabaseType" value="PubChem"/>
193 <param name="MetFragDatabaseType" value="LocalCSV"/> 214 <param name="MetFragDatabaseType" value="LocalCSV"/>
194 <param name="LocalDatabasePath" value="demo_db.csv"/> 215 <param name="LocalDatabasePath" value="demo_db.csv"/>
195 <output name="results" file="metfrag_massbank.tabular"/> 216 <output name="results" file="metfrag_massbank.tabular"/>
196 </test> 217 </test>
197 <test> 218 <test>
198 <!-- Test "generic" style data format --> 219 <!-- Test "generic" style data format -->
199 <param name="input" value="generic_format.msp"/> 220 <param name="input" value="generic_format.msp"/>
200 <param name="schema" value="msp"/> 221 <param name="schema" value="msp"/>
222 <param name="MetFragDatabaseType" value="PubChem"/>
223 <param name="skip_invalid_adducts" value="false"/>
201 <param name="MetFragDatabaseType" value="LocalCSV"/> 224 <param name="MetFragDatabaseType" value="LocalCSV"/>
202 <param name="LocalDatabasePath" value="demo_db.csv"/> 225 <param name="LocalDatabasePath" value="demo_db.csv"/>
203 <output name="results" file="metfrag_msp.tabular"/> 226 <output name="results" file="metfrag_msp.tabular"/>
204 </test> 227 </test>
205 <test> 228 <test>
206 <!-- Test PubChem API with "winter" dataset --> 229 <!-- Test PubChem API with "winter" dataset -->
207 <param name="input" value="winter_pos.msp"/> 230 <param name="input" value="winter_pos.msp"/>
208 <param name="PostProcessFilter|score_thrshld" value="0.9"/> 231 <section name="PostProcessFilter">
232 <param name="score_thrshld" value="0.9"/>
233 </section>
209 <param name="MetFragDatabaseType" value="PubChem"/> 234 <param name="MetFragDatabaseType" value="PubChem"/>
210 <output name="results" file="winter_pos.tabular"/> 235 <output name="results" file="winter_pos.tabular"/>
211 </test> 236 </test>
212 <test> 237 <test>
213 <!-- Test actual MassBank data for Glucose --> 238 <!-- Test actual MassBank data for Glucose -->
227 </test> 252 </test>
228 <test> 253 <test>
229 <!-- Test actual MassBank data for Glucose (include suspect list - default)--> 254 <!-- Test actual MassBank data for Glucose (include suspect list - default)-->
230 <param name="input" value="RP022611.txt"/> 255 <param name="input" value="RP022611.txt"/>
231 <param name="schema" value="massbank"/> 256 <param name="schema" value="massbank"/>
232 <param name="suspectlist|suspectselector" value="includesuspects"/> 257 <conditional name="suspectlist">
233 <param name="suspectlist|includesuspects_default_cond|includesuspects_default_bool" value="true"/> 258 <param name="suspectselector" value="includesuspects"/>
234 <param name="suspectlist|MetFragScoreTypes" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore"/> 259 <conditional name="includesuspects_default_cond">
235 <param name="suspectlist|MetFragScoreWeights" value="0.4,0.6,1.0"/> 260 <param name="includesuspects_default_bool" value="true"/>
261 </conditional>
262 </conditional>
236 <output name="results" file="RP022611_suspect_default.txt"/> 263 <output name="results" file="RP022611_suspect_default.txt"/>
237 </test> 264 </test>
238 <test> 265 <test>
239 <!-- Test actual MassBank data for Glucose (include suspect list - custom)--> 266 <!-- Test invalid adduct -->
240 <param name="input" value="RP022611.txt"/>
241 <param name="schema" value="massbank"/>
242 <param name="suspectlist|suspectselector" value="includesuspects"/>
243 <param name="suspectlist|includesuspects_default_cond|includesuspects_default_bool" value="false"/>
244 <param name="suspectlist|includesuspects_default_cond|ScoreSuspectLists" value="UNPD_DB.inchikeys.txt"/>
245 <param name="suspectlist|MetFragScoreTypes" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore"/>
246 <param name="suspectlist|MetFragScoreWeights" value="0.4,0.6,1.0"/>
247 <output name="results" file="RP022611_suspect_default.txt"/>
248 </test>
249 <test>
250 <!-- Test actual MassBank data for Glucose (include suspect list - custom)-->
251 <param name="input" value="invalid_adduct.msp"/> 267 <param name="input" value="invalid_adduct.msp"/>
252 <param name="skip_invalid_adducts" value="true"/> 268 <param name="skip_invalid_adducts" value="true"/>
253 <output name="results" file="invalid_adduct_result.txt"/> 269 <output name="results" file="invalid_adduct_result.txt" ftype="tabular"/>
254 </test> 270 </test>
255 </tests> 271 </tests>
256 <help> 272 <help>
257 ------- 273 -------
258 MetFrag 274 MetFrag
259 ------- 275 -------
260 276
261 Description 277 Description
262 ----------- 278 -----------
263 279
264 MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment. 280 MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is
265 281 a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases
266 Website: http://c-ruttkies.github.io/MetFrag 282 are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak
283 matches gives hints to the quality of the candidate spectrum assignment.
284
285 Website: http://ipb-halle.github.io/MetFrag/
267 286
268 Parameters 287 Parameters
269 ---------- 288 ----------
270 289
271 **\1. MSP file** 290 **\1. MSP file**
278 297
279 * KEGG 298 * KEGG
280 299
281 300
282 **\2b. MetFragDatabaseType (local CSV file database)** 301 **\2b. MetFragDatabaseType (local CSV file database)**
302
283 303
284 Custom database file in CSV format with the following structure: 304 Custom database file in CSV format with the following structure:
285 305
286 +-------------+------------------+----------+---------------------------------------------+----------------------+---+ 306 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
287 | Identifier | MonoisotopicMass | SMILES | InChI | Name |...| 307 | Identifier | MonoisotopicMass | SMILES | InChI | Name |...|
305 +---+------------------+-----------------------------+------------------+------------+-------------+ 325 +---+------------------+-----------------------------+------------------+------------+-------------+
306 |...| ... | ... | ... | ... | ... | 326 |...| ... | ... | ... | ... | ... |
307 +---+------------------+-----------------------------+------------------+------------+-------------+ 327 +---+------------------+-----------------------------+------------------+------------+-------------+
308 328
309 329
310 **\2b. MetFragDatabaseType MetChem local database** 330
331 **\2b. MetFragDatabaseType MetChem**
311 332
312 MetChem is a modified PubChem database and can be used in replace of PubChem 333 MetChem is a modified PubChem database and can be used in replace of PubChem
313 for performing API calls to the public PubChem instance. Details regarding how to serve the database can be located 334 for performing API calls to the public PubChem instance.
314 here:
315 335
316 **\3. Database Search Relative Mass Deviation - ppm** 336 **\3. Database Search Relative Mass Deviation - ppm**
317 337
318 A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses. 338 A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses.
319 339
359 379
360 **\14. PostProcessFilter** 380 **\14. PostProcessFilter**
361 381
362 To make the output more manageble results below certain criteria can be removed from the various filters can be 382 To make the output more manageble results below certain criteria can be removed from the various filters can be
363 performed on the potential compounds prior to predicting the in silico spectra 383 performed on the potential compounds prior to predicting the in silico spectra
384
385 Output
386 -------
387
388 These columns are derived from any metadata in the MSP input file (additional columns can included if they are recorded in the MSP file)
389
390 +-------------+--------------------------------------------+---+
391 | adduct | name |...|
392 +-------------+--------------------------------------------+---+
393 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
394 +-------------+--------------------------------------------+---+
395 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
396 +-------------+--------------------------------------------+---+
397 | ... | ... |...|
398 +-------------+--------------------------------------------+---+
399
400 Table continued (these columns are derived from the MetFrag result):
401
402 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
403 |...| sample_name | ExplPeaks | FormulasOfExplPeaks | ... |
404 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
405 |...| 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... |
406 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
407 |...| 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... |
408 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
409 |...| ... | ... | ... | ... |
410 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
411
412
413 Table continued (columns are derived from the MetFrag result):
414
415 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
416 |...| FragmenterScore | FragmenterScore_Values | FormulasOfExplPeaks | Identifier | InChI |...|
417 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
418 |...| 105.844569063138 | 696.0;1156.0;696.0;1156.0 | 6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 206 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H |...|
419 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
420 |...| 105.844569063138 | 696.0;1156.0;696.0;1156.0 | (3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 5793 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 |...|
421 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
422 |...| ... | ... | ... | ... | ... |...|
423 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
424
425 Table continued (columns are derived from the MetFrag result):
426
427
428 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
429 |...| NoExplPeaks | NumberPeaksUsed | OfflineMetFusionScore | SMILES | Score | SuspectListScore | XlogP3 |
430 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
431 |...| 4 | 5 | 2.84566828424078 | C(C1C(C(C(C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
432 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
433 |...| 4 | 5 | 2.84566828424078 | C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
434 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
435 |...| ... | ... | ... | ... | ... | ... | ... |
436 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
437
364 438
365 Additional notes 439 Additional notes
366 -------------------- 440 --------------------
367 441
368 The following adducts (and format) are currently supported in the MSP file. The neutral mass is automatically 442 The following adducts (and format) are currently supported in the MSP file. The neutral mass is automatically
390 - **Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)** 464 - **Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
391 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)** 465 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
392 - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)** 466 - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)**
393 - **Payam Emami (payam.emami@medsci.uu.se) - Uppsala Universitet (Sweden)** 467 - **Payam Emami (payam.emami@medsci.uu.se) - Uppsala Universitet (Sweden)**
394 - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)** 468 - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)**
395
396
397 </help> 469 </help>
398 <citations> 470 <citations>
399 <citation type="doi">10.1186/s13321-016-0115-9</citation> 471 <citation type="doi">10.1186/s13321-016-0115-9</citation>
400 </citations> 472 </citations>
401 </tool> 473 </tool>