Mercurial > repos > tomnl > mspurity_spectralmatching

annotate spectralMatching.xml @ 12:e131f2fb0f97 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
author tomnl
date Fri, 13 Sep 2019 11:48:31 -0400
parents 103d2613b3a7
children 8dd98b0f83af
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1 <tool id="mspurity_spectralmatching" name="msPurity.spectralMatching" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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2 <description>
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3 Perform spectral matching to MS/MS spectral libraries
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4 </description>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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10 <expand macro="requirements">
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11 </expand>
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14 <stdio>
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15 <exit_code range="1:" />
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16 </stdio>
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17 <command interpreter="Rscript"><![CDATA[
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18 spectralMatching.R
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19 --outDir=.
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20 --cores=\${GALAXY_SLOTS:-4}
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21
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22 #if $Query.q_dbPth_con.q_dbPth_select == 'msPurityData'
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23 --q_defaultDb
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24 #else if $Query.q_dbPth_con.q_dbPth_select == 'sqlite'
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25 --q_dbPth=$Query.q_dbPth_con.q_dbPth
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26 #end if
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28 #if $Library.l_dbPth_con.l_dbPth_select == 'msPurityData'
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29 --l_defaultDb
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30 #else if $Library.l_dbPth_con.l_dbPth_select == 'userdb_sqlite'
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31 --l_dbPth=$Library.l_dbPth_con.l_dbPth
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32 #end if
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34 --l_dbType=$Library.l_dbPth_con.l_dbPth_select
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35 --q_dbType=$Query.q_dbPth_con.q_dbPth_select
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38 --q_ppmPrec=$Query.q_filters.q_ppmPrec
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39 --l_ppmPrec=$Library.l_filters.l_ppmPrec
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41 --q_ppmProd=$Query.q_filters.q_ppmProd
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42 --l_ppmProd=$Library.l_filters.l_ppmProd
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45 #if $Query.q_filters.q_raThres_cond.q_raThres_bool
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46 --q_raThres=$Query.q_filters.q_raThres_cond.q_raThres
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47 #end if
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49 #if $Library.l_filters.l_raThres_cond.l_raThres_bool
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50 --l_raThres=$Library.l_filters.l_raThres_cond.l_raThres
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51 #end if
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52
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53 #if $Query.q_filters.q_polarity_cond.q_polarity_bool
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54 --q_polarity=$Query.q_filters.q_polarity_cond.q_polarity
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55 #end if
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57 #if $Library.l_filters.l_polarity_cond.l_polarity_bool
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58 --l_polarity=$Library.l_filters.l_polarity_cond.l_polarity
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59 #end if
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61 #if $Query.q_filters.q_purity_cond.q_purity_bool
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62 --q_purity=$Query.q_filters.q_purity_cond.q_purity
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63 #end if
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65 #if $Library.l_filters.l_purity_cond.l_purity_bool
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66 --l_purity=$Library.l_filters.l_purity_cond.l_purity
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67 #end if
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68
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69 #if $Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups_bool
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70 --q_xcmsGroups=$Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups
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71 #end if
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72
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73 #if $Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups_bool
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74 --l_xcmsGroups=$Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups
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75 #end if
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77 #if $Query.q_filters.q_pids_cond.q_pids_bool
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78 --q_pids=$Query.q_filters.q_pids_cond.q_pids
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79 #end if
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80
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81 #if $Library.l_filters.l_pids_cond.l_pids_bool
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82 --l_pids=$Library.l_filters.l_pids_cond.l_pids
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83 #end if
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84
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85 #if $Query.q_filters.q_rtrange_cond.q_rtrange_bool
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86 --q_rtrangeMin=$Query.q_filters.q_rtrange_cond.q_rtrangeMin
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87 --q_rtrangeMax=$Query.q_filters.q_rtrange_cond.q_rtrangeMax
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88 #end if
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89
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90 #if $Library.l_filters.l_rtrange_cond.l_rtrange_bool
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91 --l_rtrangeMin=$Library.l_filters.l_rtrange_cond.l_rtrangeMin
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92 --l_rtrangeMax=$Library.l_filters.l_rtrange_cond.l_rtrangeMax
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93 #end if
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94
0
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95 #if $Query.q_filters.q_accessions_cond.q_accessions_bool
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96 --q_accessions=$Query.q_filters.q_accessions_cond.q_accessions
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97 #end if
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98
0
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99 #if $Library.l_filters.l_accessions_cond.l_accessions_bool
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100 --l_accessions=$Library.l_filters.l_accessions_cond.l_accessions
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101 #end if
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102
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103
0
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104 #if $Query.q_filters.q_sources_cond.q_sources_bool
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105 --q_sources=$Query.q_filters.q_sources_cond.q_sources
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106 --q_sourcesUser=$Query.q_filters.q_sources_cond.q_sourcesUser
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107 #end if
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108
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109 #if $Library.l_filters.l_sources_cond.l_sources_bool
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110 --l_sources=$Library.l_filters.l_sources_cond.l_sources
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111 --l_sourcesUser=$Library.l_filters.l_sources_cond.l_sourcesUser
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112 #end if
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113
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114 #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool
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115 --q_instrumentTypes=$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes
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116 --q_instrumentTypesUser=$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser
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117 #end if
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118
0
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119 #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool
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120 --l_instrumentTypes=$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes
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121 --l_instrumentTypesUser=$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser
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122 #end if
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123
0
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124 #if $Query.q_filters.q_instruments_cond.q_instruments_bool
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125 --q_instruments=$Query.q_filters.q_instruments_cond.q_instruments
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126 #end if
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127
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128 #if $Library.l_filters.l_instruments_cond.l_instruments_bool
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129 --l_instruments=$Library.l_filters.l_instruments_cond.l_instruments
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130 #end if
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131
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132 #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool
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133 --q_spectraTypes=$Query.q_filters.q_spectraTypes_cond.q_spectraTypes
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134 #end if
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135
0
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136 #if $Library.l_filters.l_spectraTypes_cond.l_spectraTypes_bool
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137 --l_spectraTypes=$Library.l_filters.l_spectraTypes_cond.l_spectraTypes
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138 #end if
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139
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140 #if $Query.q_filters.q_spectraFilter
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141 --q_spectraFilter
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142 #end if
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143
0
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144 #if $Library.l_filters.l_spectraFilter
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145 --l_spectraFilter
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146 #end if
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147
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148 #if $General.rttol_cond.rttol_bool
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149 --rttol=$General.rttol_cond.rttol
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150 #end if
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151
0
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152 --raW=$General.raW
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153 --mzW=$General.mzW
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154
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155 #if $General.updateDb_cond.updateDb
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156 --updateDb
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157 #if $General.updateDb_cond.copyDb
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158 --copyDb
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159 #end if
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160 #end if
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161
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162 #if $General.usePrecursors
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163 --usePrecursors
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164 #end if
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165
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166
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167
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168 ]]></command>
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169 <inputs>
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170
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171
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172
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173 <section name="Query" title="Query spectra input and filters" expanded="True">
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174 <expand macro="sm_input" ql='Query' ql_shrt = "q" user="True" mspuritydatalib="False" msp="False"
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175 help="Query SQLite database - in the standard XCMS msPurity workflow - the output
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176 of msPurity.createDatabase should be used here. However any SQLite database
0
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177 following the schema of xxx can be used as input"/>
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178 <expand macro="filters" ql="Query" ql_shrt="q"/>
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179 </section>
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180
0
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181 <section name="Library" title="Library spectra input and filters" expanded="True">
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182 <expand macro="sm_input" ql='Library' ql_shrt = "l" user="False" mspuritydatalib="True" msp="False"
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183 help="Library SQLite database - in the standard XCMS msPurity workflow - a default
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184 database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite
0
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185 database following the schema of xxx can be used as input"/>
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186 <expand macro="filters" ql="Library" ql_shrt="l"/>
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187 </section>
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188
0
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189 <section name="General" title="General arguments" expanded="False">
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190 <conditional name="rttol_cond">
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191 <param name="rttol_bool" type="boolean" label="Filter on retention time match?"
0
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192 help="" />
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193 <when value="true">
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194 <param name="rttol" type="float" value="30" min="0"
0
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195 label="Retention time tolerance (seconds)"
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196 help="Retention time tolerance in seconds to match precursors"/>
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197 </when>
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198 <when value="false">
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199 </when>
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200 </conditional>
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201
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202
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203 <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?"
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204 help="If True, spectra will be filtered by similarity of precursors based on
0
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205 the library and query ppm defined tolerance" />
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206
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207 <param name="raW" label="Weighting for relative abundance"
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208 type="float" value="0.5"
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209 help="Relative abundance weight for spectra (default to 0.5 as determined by
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210 massbank for ESI data)"/>
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211
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212 <param name="mzW" label="Weighting for mz"
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213 type="float" value="2"
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214 help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/>
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215
0
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216 <conditional name="updateDb_cond">
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217 <param name="updateDb" type="boolean" checked="true"
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218 label="Update database with results?" help="" />
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219 <when value="true">
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220 <param name="copyDb" type="boolean" checked="true"
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221 label="Make a copy of the database?"
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222 help="A copy will be made of the input SQLite target database and the
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223 results will be added to this copy. When False, the input SQLite
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224 database will be updated with the matching results. Use False if
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225 you want to reduce storage space being used."/>
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226 </when>
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227 <when value="false">
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228 </when>
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229 </conditional>
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230
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231
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232
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233 </section>
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234
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235
0
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236
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237
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238 </inputs>
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239
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240 <outputs>
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241 <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results"
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242 from_work_dir="db_with_spectral_matching.sqlite" >
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243 <filter>create_new_database is True</filter>
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244 </data>
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245 <data name="matches" format="tsv" label="${tool.name} on ${on_string}: matches"
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246 from_work_dir="matched_results.tsv" >
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247 <filter>spectra_type_q == "scans"</filter>
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248 </data>
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249 <data name="xcms_matches" format="tsv" label="${tool.name} on ${on_string}: XCMS matches"
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250 from_work_dir="xcms_matched_results.tsv" />
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251 </outputs>
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252 <tests>
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253 <test>
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254 <param name="q_dbPth" value="createDatabase_output.sqlite" />
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255 <param name="l_dbPth_select" value="userdb" />
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256 <param name="l_dbPth" value="PR100037.sqlite" />
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257
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258 <param name="q_xcmsGroups_bool" value="true" />
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259 <param name="l_accessions_bool" value="true" />
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260 <param name="q_xcmsGroups" value="14" />
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261 <param name="l_accessions" value="PR100037" />
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262 <output name="xcms_matches" file="spectralMatching_matched_results.tsv" />
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263 <output name="matches" file="spectralMatching_xcms_matched_results.tsv" />
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264 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/>
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265 </test>
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266 </tests>
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267
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268
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269
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270 <help><![CDATA[
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271
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272 =============================================================
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273 Spectral matching
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274 =============================================================
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275 -----------
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276 General
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277 -----------
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278
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279
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280 Perform spectral matching to spectral libraries for an LC-MS/MS dataset.
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281
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282 The spectral matching is performed from a **Query** SQLite spectral-database against a **Library** SQLite spectral-database.
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283
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284 The SQLite schema of the spectral database here: spectral_database_schema_
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285
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286
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287 The query spectral-database in most cases should contain be the "unknown" spectra database generated the msPurity
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288 function createDatabase as part of a msPurity-XCMS data processing workflow.
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289
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290 The library spectral-database in most cases should contain the "known" spectra from either public or user generated resources.
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291 The library SQLite database by default contains data from MoNA including Massbank, HMDB, LipidBlast and GNPS.
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292 A larger_database_ can be download and used from the msp2db github repository.
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293
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294 To create a user generated library SQLite database the following tool can be used to generate a SQLite database
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295 from a collection of MSP files: msp2db_.
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296
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297 It should be noted though, that as long as the schema of the spectral-database is as described here, then any database can be used
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298 for either the library or query - even allowing for the same database to be used.
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299
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300 The spectral matching functionality has four main components, spectral filtering, spectral alignment, spectral matching,
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301 and summarising the results.
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302
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303 Spectral filtering is simply filtering both the library and query spectra to be search against (e.g. choosing
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304 the library source, instrument, retention time, precursor PPM tolerance etc).
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305
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306 The spectral alignment stage involves aligning the query peaks to the library peaks. The approach used is similar
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307 to modified pMatch algorithm described in Zhou et al 2015.
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308
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309 The spectral matching of the aligned spectra is performed against a combined intensity and m/z weighted vector - created for both
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310 the query and library spectra (wq and wl). See below:
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311
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312 .. math::
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313
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314 w=intensity^x \cdot mz^y
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315
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316
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317 Where x and y represent weight factors and can be adjusted with the parameters raW and mzW.
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318 Defaults to x=0.5 and y=2 as per MassBank for ESI based mass spectrometry data.
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319
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320 The aligned weighted vectors are then matched using dot product cosine, reverse dot product cosine and the composite dot product.
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321 See below for dot product cosine equation.
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322
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323 .. math::
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324
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325 dpc = \frac{ w_q \cdot w_l } { \sqrt{Σ{w_{q}{}^2} } \cdot \sqrt{Σ{w_{l}{}^2}}}
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326
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327
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328 Full details of the matching approaches are described in the msPurity_spectral_matching_vignette_
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329
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330 --------------------------------------------
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331 Example LC-MS/MS processing workflow
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332 --------------------------------------------
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333
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334 * Purity assessments
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335 + (mzML files) -> purityA -> (pa)
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336 * XCMS processing
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337 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
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338 * Fragmentation processing
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339 + (xset, pa) -> frag4feature -> filterFragSpectra -> averageAllFragSpectra -> createDatabase -> **spectralMatching** -> (sqlite spectral database)
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340
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341 -----------
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342 Output
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343 -----------
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344
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345 **Database**
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346
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347 The updated query database (this will have been updated with the annotation results if updateDb argument used)
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348
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349
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350 **xcmsMatchedResults**
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351
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352 If the qeury spectra had XCMS based chromotographic peaks tables (e.g c_peak_groups, c_peaks) in the sqlite database - it will
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353 be possible to summarise the matches for each XCMS grouped feature. The dataframe contains the following columns
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354
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355 * lpid - id in database of library spectra
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356 * qpid - id in database of query spectra
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357 * dpc - dot product cosine of the match
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358 * rdpc - reverse dot product cosine of the match
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359 * cdpc - composite dot product cosine of the match
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360 * mcount - number of matching peaks
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361 * allcount - total number of peaks across both query and library spectra
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362 * mpercent - percentage of matching peaks across both query and library spectra
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363 * library_rt - retention time of library spectra
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364 * query_rt - retention time of query spectra
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365 * rtdiff - difference between library and query retention time
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366 * library_precursor_mz - library precursor mz
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367 * query_precursor_mz - query precursor mz
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368 * library_precursor_ion_purity - library precursor ion purity
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369 * query_precursor_ion_purity - query precursor ion purity
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370 * library_accession - library accession value (unique string or number given to eith MoNA or Massbank data entires)
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371 * library_precursor_type - library precursor type (i.e. adduct)
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372 * library_entry_name - Name given to the library spectra
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373 * inchikey - inchikey of the matched library spectra
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374 * library_source_name - source of the spectra (e.g. massbank, gnps)
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375 * library_compound_name - name of compound spectra was obtained from
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376
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377 **matchedResults**
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378
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379 All matched results from the query spectra to the library spectra. Contains the same as above
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380 without the XCMS details. This table is useful to observe spectral matching results
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381 for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features.
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382
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383
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384 .. _spectral_database_schema: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html
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385 .. _larger_database: https://github.com/computational-metabolomics/msp2db/releases
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386 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases
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387 .. _msPurity_spectral_matching_vignette: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
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388
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389 ]]></help>
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390
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391 <expand macro="citations"> </expand>
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392 </tool>