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annotate metfrag.xml @ 3:5ee936e570a7 draft

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planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b5d5fdc81a1756000dc25d4aa672fec1ece732a
author tomnl
date Tue, 25 Jun 2019 06:02:26 -0400
parents d040e27b6225
children eb581a101672
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1 <tool id="metfrag" name="MetFrag" version="0.1.8">
0
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2 <description> </description>
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3 <requirements>
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4 <requirement type="package" version="2.4.2">metfrag</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
1
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9 python $__tool_directory__/metfrag.py
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10 --input_pth "$input"
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11 --result_pth '$results'
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12 --temp_dir './temp/'
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14 --cores_top_level \${GALAXY_SLOTS:-4}
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16 --MetFragDatabaseType '$db_select.MetFragDatabaseType'
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18 #if $db_select.MetFragDatabaseType == "LocalCSV":
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19 --LocalDatabasePath '$db_select.LocalDatabasePath'
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20 #elif $db_select.MetFragDatabaseType == "MetChem":
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21 --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp'
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22 #end if
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24 --DatabaseSearchRelativeMassDeviation $DatabaseSearchRelativeMassDeviation
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25 --FragmentPeakMatchRelativeMassDeviation $FragmentPeakMatchRelativeMassDeviation
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26 --FragmentPeakMatchAbsoluteMassDeviation $FragmentPeakMatchAbsoluteMassDeviation
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27 --polarity '$polarity'
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28
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29 --MetFragScoreTypes '$suspectlist.MetFragScoreTypes'
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30 --MetFragScoreWeights '$suspectlist.MetFragScoreWeights'
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31 --ScoreSuspectLists '$suspectlist.ScoreSuspectLists'
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32
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33 --meta_select_col $meta_select_col
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34 --minMSMSpeaks $minMSMSpeaks
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35 --schema $schema
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36
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37 $PreProcessFilter.UnconnectedCompoundFilter
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38 $PreProcessFilter.IsotopeFilter
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39
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41 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements'
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42 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements'
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43 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList'
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44 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList'
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45 --FilterIncludedElements '$PreProcessFilter.FilterIncludedElements'
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46 --FilterExcludedElements '$PreProcessFilter.FilterExcludedElements'
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47 --FilterIncludedExclusiveElements '$PreProcessFilter.FilterIncludedExclusiveElements'
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48
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49 --score_thrshld $PostProcessFilter.score_thrshld
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50 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld
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51
0
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52 ]]></command>
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53 <inputs>
1
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54
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55 <param name="input" type="data" format="msp,txt" label="MSP file (Output from Create MSP tool)"/>
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56 <conditional name="db_select">
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57 <param name="MetFragDatabaseType" type="select" label="Choose Compound Database"
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58 argument="--MetFragDatabaseType">
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59 <option value="PubChem" selected="true">PubChem</option>
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60 <option value="KEGG">KEGG</option>
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61 <option value="LocalCSV">Local database (csv)</option>
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62 <option value="MetChem">MetChem</option>
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63 </param>
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64 <when value="MetChem">
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65 <param name="LocalMetChemDatabaseServerIp" type="text" label="MetChem URL"
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66 argument="--LocalMetChemDatabaseServerIp" />
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67 </when>
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68 <when value="LocalCSV">
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69 <param name="LocalDatabasePath" type="data" format="csv" label="Local database of compounds (CSV format)" argument="--LocalDatabasePath"/>
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70 </when>
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71 <when value="KEGG">
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72 </when>
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73 <when value="PubChem">
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74 </when>
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75 </conditional>
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76 <param name="DatabaseSearchRelativeMassDeviation" type="float" value="10"
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77 label="Relative Mass Deviation for database search (ppm)" argument="--DatabaseSearchRelativeMassDeviation"
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78 help="A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses"/>
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79 <param name="FragmentPeakMatchRelativeMassDeviation" type="float" value="5"
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80 label="Fragment Peak Match Relative Mass Deviation (ppm)" argument="--FragmentPeakMatchRelativeMassDeviation"
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81 help="Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks" />
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82 <param name="FragmentPeakMatchAbsoluteMassDeviation" type="float" value="0.001"
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83 label="Fragment Peak Match Absolute Mass Deviation (Da)" argument="FragmentPeakMatchAbsoluteMassDeviation"
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84 help="Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks" />
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85 <param name="polarity" type="select" label="Polarity" help="The polarity used for the mode of acquisition">
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86 <option value="pos" selected="true">Positive</option>
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87 <option value="neg">Negative</option>
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88 </param>
1
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89 <param name="schema" type="select" label="Schema"
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90 help="The schema used for the MSP file (auto will try automatically determine the schema)">
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91 <option value="auto" selected="True">Auto</option>
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92 <option value="msp" >Generic MSP</option>
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93 <option value="massbank">MassBank</option>
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94 </param>
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95 <param name="meta_select_col" type="select" label="Choose how additional metadata columns are extracted"
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96 help="The MetFrag output can have additional meta data columns added, these can be either extracted
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97 from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns
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98 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and :
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99 e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns">
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100 <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option>
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101 <option value="name_split" >Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option>
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102 <option value="all">Extra metadata columns from all MSP parameters</option>
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103 </param>
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104
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105 <conditional name="suspectlist">
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106 <param name="suspectselector" type="select" optional="False" label="Suspect list" help="Choose whether to include a suspect list">
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107 <option value="includesuspects" >Include suspect list</option>
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108 <option value="excludesuspects" selected="True">Do not include suspect list</option>
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109 </param>
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110 <when value="includesuspects">
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111 <param name="ScoreSuspectLists" type="data" format="txt" optional="False" label="Suspect list file" help="File containing a list of suspects" />
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112 <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." />
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113 <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." />
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114 </when>
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115 <when value="excludesuspects">
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116 <param name="ScoreSuspectLists" type="select" optional="False" label="Suspect list file" help="File containing a list of suspects">
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117 <option value="None" selected="True">No suspect list file</option>
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118 </param>
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119 <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." />
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120 <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." />
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121 </when>
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122 </conditional>
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123
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124 <param name="minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/>
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125 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False">
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126 <param name="UnconnectedCompoundFilter" type="boolean" checked="false" truevalue="--UnconnectedCompoundFilter"
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127 falsevalue="" label="filter non-connected compounds (e.g. salts)" help=""/>
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128 <param name="IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter" falsevalue=""
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129 label="filter compounds containing non-standard isotopes" help=""/>
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130 <param name="FilterMinimumElements" type="text" label="Minimum Elements Filter"
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131 help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least 2 nitrogens and 3 oxygens"/>
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132 <param name="FilterMaximumElements" type="text" label="Maximum Elements Filter"
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133 help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at maximum 5 nitrogens and 7 oxygens"/>
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134 <param name="FilterSmartsInclusionList" type="text" label="Include substructures"
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135 help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds containing benzene"/>
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136 <param name="FilterSmartsExclusionList" type="text" label="Exclude substructures"
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137 help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds containing hydroxyl groups"/>
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138 <param name="FilterIncludedElements" type="text" label="Include elements"
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139 help="Filter by presence of defined elements (other elements are allowed). Ex: 'N,O' include compounds containing nitrogen and oxygen" />
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140 <param name="FilterIncludedExclusiveElements" type="text" label="Include elements (exclusive)"
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141 help="Filter by presence of defined elements (no other elements are allowed). Ex: 'N,O' include compounds only composed of nitrogen and oxygen" />
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142 <param name="FilterExcludedElements" type="text" label="Exclude elements"
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143 help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out compounds including bromine or chlorine"/>
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144 </section>
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145
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146 <section name="PostProcessFilter" title="PostProcessing filters" expanded="False">
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147 <param name="score_thrshld" type="float" label="Threshold for score after MetFrag search" max="1" min="0" value="0"/>
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148 <param name="pctexplpeak_thrshld" type="integer" label="Minimum percentage of explain peaks" max="100" min="0" value="0"/>
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149 </section>
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150
0
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151 </inputs>
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152 <outputs>
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153 <data name="results" format="tabular" label="${tool.name} results of ${input.name}" />
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154 </outputs>
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155 <tests>
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156 <test>
1
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157 <param name="input" value="massbank_format.txt"/>
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158 <param name="schema" value="massbank"/>
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159 <param name="MetFragDatabaseType" value="LocalCSV"/>
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160 <param name="LocalDatabasePath" value="demo_db.csv"/>
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161 <output name="results" file="metfrag_massbank.tabular"/>
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162 </test>
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163 <test>
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164 <param name="input" value="generic_format.msp"/>
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165 <param name="schema" value="msp"/>
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166 <param name="MetFragDatabaseType" value="LocalCSV"/>
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167 <param name="LocalDatabasePath" value="demo_db.csv"/>
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168 <output name="results" file="metfrag_msp.tabular"/>
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169 </test>
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170 <test>
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171 <param name="input" value="FU000001.txt"/>
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172 <param name="MetFragDatabaseType" value="LocalCSV"/>
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173 <param name="LocalDatabasePath" value="demo_db.csv"/>
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174 <output name="results" file="FU000001.tabular"/>
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175 </test>
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176 <test>
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177 <param name="input" value="winter_pos.msp"/>
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178 <param name="PostProcessFilter|score_thrshld" value="0.9"/>
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179 <param name="MetFragDatabaseType" value="PubChem"/>
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180 <output name="results" file="winter_pos.tabular"/>
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181 </test>
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182 <test>
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183 <param name="input" value="FU000001.txt"/>
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184 <param name="schema" value="massbank"/>
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185 <param name="MetFragDatabaseType" value="LocalCSV"/>
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186 <param name="LocalDatabasePath" value="demo_db.csv"/>
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187 <param name="meta_select_col" value="all"/>
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188 <output name="results" file="FU000001_all_col.tabular"/>
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189 </test>
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190 <test>
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191 <param name="input" value="FU000001.txt"/>
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192 <param name="schema" value="massbank"/>
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193 <param name="suspectlist|suspectselector" value="includesuspects"/>
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194 <param name="suspectlist|ScoreSuspectLists" value="UNPD_DB.inchikeys.txt"/>
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195 <param name="suspectlist|MetFragScoreTypes" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore"/>
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196 <param name="suspectlist|MetFragScoreWeights" value="0.4,0.6,1.0"/>
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197 <output name="results" file="FU000001_suspect.txt"/>
0
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198 </test>
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199 </tests>
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200 <help>
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201 -------
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202 MetFrag
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203 -------
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204
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205 Description
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206 -----------
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207
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208 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.
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209
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210 Website: http://c-ruttkies.github.io/MetFrag
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211
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212 Parameters
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213 ----------
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214
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215 **\1. MSP file**
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216
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217 MSP file created using *Create MSP* tool
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218
1
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219 **\2a. MetFragDatabaseType (public databases)**
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220
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221 * PubChem
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222
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223 * KEGG
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224
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225
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226 **\2b. MetFragDatabaseType (local CSV file database)**
0
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227
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228 Custom database file in CSV format with the following structure:
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229
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230 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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231 | Identifier | MonoisotopicMass | SMILES | InChI | Name |...|
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232 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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233 | HMDB0000123 | 75.03202841 | NCC(O)=O | InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) | Glycine |...|
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234 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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235 | HMDB0002151 | 78.0139355 | CS(C)=O | InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 | Dimethyl sulfoxide |...|
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236 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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237 | ... | ... | ... | ... | ... |...|
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238 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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239
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240
1
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241 Table continued:
0
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242
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243 +---+------------------+-----------------------------+------------------+------------+-------------+
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244 |...| MolecularFormula | InChIKey | InChIKey1 | InChIKey2 | InChIKey3 |
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245 +---+------------------+-----------------------------+------------------+------------+-------------+
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246 |...| C2H5NO2 | DHMQDGOQFOQNFH-UHFFFAOYSA-N | DHMQDGOQFOQNFH | UHFFFAOYSA | N |
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247 +---+------------------+-----------------------------+------------------+------------+-------------+
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248 |...| C2H6OS | IAZDPXIOMUYVGZ-UHFFFAOYSA-N | IAZDPXIOMUYVGZ | UHFFFAOYSA | N |
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249 +---+------------------+-----------------------------+------------------+------------+-------------+
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250 |...| ... | ... | ... | ... | ... |
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251 +---+------------------+-----------------------------+------------------+------------+-------------+
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252
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253
1
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254 **\2b. MetFragDatabaseType MetChem local database**
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255
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256 MetChem is a modified PubChem database and can be used in replace of PubChem
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257 for performing API calls to the public PubChem instance. Details regarding how to serve the database can be located
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258 here:
0
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259
1
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260 **\3. Database Search Relative Mass Deviation - ppm**
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261
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262 A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses.
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263
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264 **\4. Fragment Peak Match Relative Mass Deviation - ppm**
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265
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266 Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks.
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267
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268 **\5. Fragment Peak Match Absolute Mass Deviation (Da)**
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269
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270 Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks.
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271
1
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272 **\6. Polarity**
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273
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274 The polarity used for the mode of acquisition.
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275
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276 **\7. Schema**
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277
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278 The Schema used by the MSP file (e.g. generic MSP format or MassBank format)
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279
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280 **\8. Suspect list**
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281
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282 Choose whether to include a file containing a list of suspects.
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283
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284 **\9. MetFrag Score Types**
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285
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286 The type of scores MetFrac is using for the calculations. Please do not change the values unless you know what you are doing!
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287
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288 **\10. MetFrag Score Weights**
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289
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290 The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100%.
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291
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292 **\11. MetFrag Database Type**
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293
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294 Database to choose from.
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295
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296 **\12. minMSMSpeaks**
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297
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298 Minimum MS/MS peaks within a MS/MS spectra to be used for the MetFrag calculation
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299
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300 **\13. PreProcessFilter**
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301
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302 Various filters can be performed on the potential compounds prior to predicting the in silico spectra
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303
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304 **\14. PostProcessFilter**
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305
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306 To make the output more manageble results below certain criteria can be removed from the pVarious filters can be performed on the potential compounds prior to predicting the in silico spectra
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307
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308
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309 Developers and contributors
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310 ---------------------------
1
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311 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
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312 - **Julien Saint-Vanne (julien.saint-vanne@sb-roscoff.fr) - ABiMS (France)**
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313 - **Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
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314 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
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315 - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)**
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316 - **Payam Emami (payam.emami@medsci.uu.se) - Uppsala Universitet (Sweden)**
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317 - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)**
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318
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319
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320 </help>
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321 <citations>
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322 <citation type="doi">10.1186/s13321-016-0115-9</citation>
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323 </citations>
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324 </tool>