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annotate metfrag.xml @ 9:5763234618d4 draft default tip

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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
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9
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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1 <tool id="metfrag" name="MetFrag" version="2.4.5+galaxy1">
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2 <description>
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3 in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="2.4.5">metfrag</requirement>
0
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10 </requirements>
4
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11 <stdio>
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12 <regex match="Cannot allocate memory"
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13 source="stderr"
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14 level="fatal_oom"
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15 description="Out of memory error occurred" />
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16 </stdio>
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17 <command detect_errors="exit_code">
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18 <![CDATA[
9
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19 python '$__tool_directory__/metfrag.py'
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20 --input_pth '$input'
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21 --result_pth '$results'
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22 --temp_dir './temp/'
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24 --cores_top_level \${GALAXY_SLOTS:-4}
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25
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26 --MetFragDatabaseType '$db_select.MetFragDatabaseType'
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27
9
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28 #if $db_select.MetFragDatabaseType == 'LocalCSV':
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29 --LocalDatabasePath '$db_select.LocalDatabasePath'
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30 #elif $db_select.MetFragDatabaseType == 'MetChem':
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31 --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp'
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32 #end if
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33
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34 --DatabaseSearchRelativeMassDeviation $DatabaseSearchRelativeMassDeviation
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35 --FragmentPeakMatchRelativeMassDeviation $FragmentPeakMatchRelativeMassDeviation
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36 --FragmentPeakMatchAbsoluteMassDeviation $FragmentPeakMatchAbsoluteMassDeviation
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37 --polarity '$polarity'
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38
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39 --MetFragScoreTypes '$suspectlist.MetFragScoreTypes'
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40 --MetFragScoreWeights '$suspectlist.MetFragScoreWeights'
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41
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42 #if $suspectlist.suspectselector == 'includesuspects':
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43 #if $suspectlist.includesuspects_default_cond:
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44 --ScoreSuspectLists '$__tool_directory__/UNPD_DB.inchikeys.txt'
4
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45 #else
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46 --ScoreSuspectLists '$suspectlist.includesuspects_custom_cond.ScoreSuspectLists'
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47 #end if
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48 #end if
1
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49
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50 --meta_select_col $meta_select_col
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51 --minMSMSpeaks $minMSMSpeaks
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52 --schema $schema
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53
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54 $PreProcessFilter.UnconnectedCompoundFilter
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55 $PreProcessFilter.IsotopeFilter
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56
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57 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements'
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58 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements'
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59 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList'
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60 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList'
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61 --FilterIncludedElements '$PreProcessFilter.FilterIncludedElements'
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62 --FilterExcludedElements '$PreProcessFilter.FilterExcludedElements'
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63 --FilterIncludedExclusiveElements '$PreProcessFilter.FilterIncludedExclusiveElements'
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64
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65 $skip_invalid_adducts
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66 --score_thrshld $PostProcessFilter.score_thrshld
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67 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld
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68
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69 ]]></command>
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70 <inputs>
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71 <param name="input" type="data" format="msp" label="MSP file (Output from Create MSP tool)"/>
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72 <conditional name="db_select">
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73 <param argument="--MetFragDatabaseType" type="select" label="Choose Compound Database">
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74 <option value="PubChem" selected="true">PubChem</option>
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75 <option value="KEGG">KEGG</option>
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76 <option value="LocalCSV">Local database (csv)</option>
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77 <option value="MetChem">MetChem</option>
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78 </param>
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79 <when value="MetChem">
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80 <param argument="--LocalMetChemDatabaseServerIp" type="text" label="MetChem URL"/>
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81 </when>
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82 <when value="LocalCSV">
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83 <param argument="--LocalDatabasePath" type="data" format="csv"
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84 label="Local database of compounds (CSV format)" />
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85 </when>
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86 <when value="KEGG"/>
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87 <when value="PubChem"/>
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88 </conditional>
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89 <param argument="--DatabaseSearchRelativeMassDeviation" type="float" min="0" value="10"
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90 label="Relative Mass Deviation for database search (ppm)"
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91 help="A value in ppm that defines the deviation of theoretical masses in the database
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92 vs. the measured masses"/>
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93 <param argument="--FragmentPeakMatchRelativeMassDeviation" type="float" min="0" value="5"
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94 label="Fragment Peak Match Relative Mass Deviation (ppm)"
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95 help="Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks" />
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96 <param argument="--FragmentPeakMatchAbsoluteMassDeviation" type="float" min="0" value="0.001"
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97 label="Fragment Peak Match Absolute Mass Deviation (Da)"
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98 help="Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks" />
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99 <param argument="--polarity" type="select" label="Polarity"
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100 help="The polarity used for the mode of acquisition">
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101 <option value="pos" selected="true">Positive</option>
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102 <option value="neg">Negative</option>
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103 </param>
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104 <param argument="--schema" type="select" label="Schema"
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105 help="The schema used for the MSP file (auto will try automatically determine the schema)">
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106 <option value="auto" selected="True">Auto</option>
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107 <option value="msp">Generic MSP</option>
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108 <option value="massbank">MassBank</option>
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109 </param>
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110 <param argument="--meta_select_col" type="select"
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111 label="Choose how additional metadata columns are extracted"
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112 help="The MetFrag output can have additional meta data columns added, these can be either extracted
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113 from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns
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114 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and :
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115 e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns">
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116 <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option>
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117 <option value="name_split">Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option>
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118 <option value="all">Extra metadata columns from all MSP parameters</option>
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119 </param>
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120 <conditional name="suspectlist">
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121 <param name="suspectselector" type="select" label="Suspect list"
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122 help="Choose whether to include a suspect list">
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123 <option value="includesuspects" >Include suspect list</option>
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124 <option value="excludesuspects" selected="True">Do not include suspect list</option>
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125 </param>
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126 <when value="includesuspects">
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127 <conditional name="includesuspects_default_cond">
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128 <param name="includesuspects_default_bool" type="boolean"
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129 label="Use default list of suspect compounds?"
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130 help="Either provide a file containing a list of suspect compounds or a default file
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131 of an aggregated list of in silico predicted MS/MS spectra of natural products
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132 from the Universal Natural Products Database (http://pkuxxj.pku.edu.cn/UNPD/index.php).
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133 The list is an aggregated version of the github repository https://github.com/oolonek/ISDB/tree/master/Data/dbs."/>
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134 <when value="true"/>
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135 <when value="false">
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136 <param argument="--ScoreSuspectLists" type="data" format="txt" optional="True"
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137 label="Suspect list file" help="File containing a list of suspects inchikeys" />
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138 </when>
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139 </conditional>
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140 <expand macro="metfrag_scoring"/>
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141 </when>
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142 <when value="excludesuspects">
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143 <expand macro="metfrag_scoring" suspectlistscore="False" weights="1.0,1.0"/>
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144 </when>
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145 </conditional>
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146 <param argument="--minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/>
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147 <param argument="--skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?"
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148 truevalue="--skip_invalid_adducts" falsevalue="" checked="true"
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149 help="If no adduct type is provided within the MSP file or if the adduct type is not usable
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150 with MetFrag, set to 'yes' if these spectra should be skipped or 'no' if the default
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151 of [M+H]+ for pos data or [M-H]- for neg data should be used"/>
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152 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False">
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153 <param argument="--UnconnectedCompoundFilter" type="boolean" checked="false"
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154 truevalue="--UnconnectedCompoundFilter" falsevalue=""
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155 label="filter non-connected compounds (e.g. salts)" help=""/>
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156 <param argument="--IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter"
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157 falsevalue="" label="filter compounds containing non-standard isotopes" help=""/>
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158 <param argument="--FilterMinimumElements" type="text"
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159 optional="true" label="Minimum Elements Filter"
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160 help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least
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161 2 nitrogens and 3 oxygens">
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162 <expand macro="text-alphanumeric-regex-validator"/>
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163 </param>
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164 <param argument="--FilterMaximumElements" type="text"
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165 optional="true" label="Maximum Elements Filter"
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166 help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at
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167 maximum 5 nitrogens and 7 oxygens">
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168 <expand macro="text-alphanumeric-regex-validator"/>
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169 </param>
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170 <param argument="--FilterSmartsInclusionList" type="text"
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171 optional="true" label="Include substructures"
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172 help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds
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173 containing benzene"/>
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174 <param argument="--FilterSmartsExclusionList" type="text"
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175 optional="true" label="Exclude substructures"
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176 help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds
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177 containing hydroxyl groups"/>
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178 <param argument="--FilterIncludedElements" type="text"
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179 optional="true" label="Include elements"
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180 help="Filter by presence of defined elements (other elements are allowed).
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181 Ex: 'N,O' include compounds containing nitrogen and oxygen" >
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182 <expand macro="text-alphanumeric-comma-regex-validator"/>
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183 </param>
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184 <param argument="--FilterIncludedExclusiveElements" type="text"
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185 optional="true" label="Include elements (exclusive)"
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186 help="Filter by presence of defined elements (no other elements are allowed).
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187 Ex: 'N,O' include compounds only composed of nitrogen and oxygen" >
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188 <expand macro="text-alphanumeric-comma-regex-validator"/>
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189 </param>
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190 <param argument="--FilterExcludedElements" type="text"
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191 optional="true" label="Exclude elements"
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192 help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out
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193 compounds including bromine or chlorine">
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194 <expand macro="text-alphanumeric-comma-regex-validator"/>
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195 </param>
1
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196 </section>
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197 <section name="PostProcessFilter" title="PostProcessing filters" expanded="False">
9
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198 <param argument="--score_thrshld" type="float" label="Threshold for score after MetFrag search"
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199 max="1" min="0" value="0"/>
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200 <param argument="--pctexplpeak_thrshld" type="float" label="Minimum percentage of explain peaks"
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201 max="100" min="0" value="0"/>
1
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202 </section>
0
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203 </inputs>
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204 <outputs>
9
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205 <data name="results" format="tabular"/>
0
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206 </outputs>
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207 <tests>
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208 <test>
4
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209 <!-- Test "massbank" style data format -->
1
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210 <param name="input" value="massbank_format.txt"/>
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211 <param name="schema" value="massbank"/>
9
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212 <param name="skip_invalid_adducts" value="false"/>
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213 <param name="MetFragDatabaseType" value="PubChem"/>
1
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214 <param name="MetFragDatabaseType" value="LocalCSV"/>
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215 <param name="LocalDatabasePath" value="demo_db.csv"/>
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216 <output name="results" file="metfrag_massbank.tabular"/>
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217 </test>
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218 <test>
4
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219 <!-- Test "generic" style data format -->
1
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220 <param name="input" value="generic_format.msp"/>
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221 <param name="schema" value="msp"/>
9
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222 <param name="MetFragDatabaseType" value="PubChem"/>
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223 <param name="skip_invalid_adducts" value="false"/>
1
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224 <param name="MetFragDatabaseType" value="LocalCSV"/>
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225 <param name="LocalDatabasePath" value="demo_db.csv"/>
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226 <output name="results" file="metfrag_msp.tabular"/>
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227 </test>
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228 <test>
4
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229 <!-- Test PubChem API with "winter" dataset -->
1
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230 <param name="input" value="winter_pos.msp"/>
9
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231 <section name="PostProcessFilter">
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232 <param name="score_thrshld" value="0.9"/>
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233 </section>
1
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234 <param name="MetFragDatabaseType" value="PubChem"/>
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235 <output name="results" file="winter_pos.tabular"/>
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236 </test>
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237 <test>
4
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238 <!-- Test actual MassBank data for Glucose -->
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239 <param name="input" value="RP022611.txt"/>
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240 <param name="MetFragDatabaseType" value="LocalCSV"/>
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241 <param name="LocalDatabasePath" value="demo_db.csv"/>
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242 <output name="results" file="RP022611.tabular"/>
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243 </test>
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244 <test>
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245 <!-- Test actual MassBank data for Glucose (all metadata columns in output-->
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246 <param name="input" value="RP022611.txt"/>
1
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247 <param name="schema" value="massbank"/>
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248 <param name="MetFragDatabaseType" value="LocalCSV"/>
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249 <param name="LocalDatabasePath" value="demo_db.csv"/>
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250 <param name="meta_select_col" value="all"/>
4
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251 <output name="results" file="RP022611_all_col.tabular"/>
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252 </test>
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253 <test>
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254 <!-- Test actual MassBank data for Glucose (include suspect list - default)-->
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255 <param name="input" value="RP022611.txt"/>
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256 <param name="schema" value="massbank"/>
9
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257 <conditional name="suspectlist">
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258 <param name="suspectselector" value="includesuspects"/>
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259 <conditional name="includesuspects_default_cond">
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260 <param name="includesuspects_default_bool" value="true"/>
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261 </conditional>
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262 </conditional>
4
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263 <output name="results" file="RP022611_suspect_default.txt"/>
1
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264 </test>
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265 <test>
9
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266 <!-- Test invalid adduct -->
4
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267 <param name="input" value="invalid_adduct.msp"/>
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268 <param name="skip_invalid_adducts" value="true"/>
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269 <output name="results" file="invalid_adduct_result.txt" ftype="tabular"/>
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270 </test>
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271 </tests>
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272 <help>
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273 -------
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274 MetFrag
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275 -------
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276
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277 Description
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278 -----------
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279
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280 MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is
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281 a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases
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282 are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak
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283 matches gives hints to the quality of the candidate spectrum assignment.
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284
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285 Website: http://ipb-halle.github.io/MetFrag/
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286
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287 Parameters
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288 ----------
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289
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290 **\1. MSP file**
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291
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292 MSP file created using *Create MSP* tool
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293
1
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294 **\2a. MetFragDatabaseType (public databases)**
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295
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296 * PubChem
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297
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298 * KEGG
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299
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300
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301 **\2b. MetFragDatabaseType (local CSV file database)**
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302
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303
0
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304 Custom database file in CSV format with the following structure:
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305
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306 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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307 | Identifier | MonoisotopicMass | SMILES | InChI | Name |...|
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308 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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309 | HMDB0000123 | 75.03202841 | NCC(O)=O | InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) | Glycine |...|
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310 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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311 | HMDB0002151 | 78.0139355 | CS(C)=O | InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 | Dimethyl sulfoxide |...|
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312 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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313 | ... | ... | ... | ... | ... |...|
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314 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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315
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316
1
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317 Table continued:
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318
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319 +---+------------------+-----------------------------+------------------+------------+-------------+
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320 |...| MolecularFormula | InChIKey | InChIKey1 | InChIKey2 | InChIKey3 |
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321 +---+------------------+-----------------------------+------------------+------------+-------------+
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322 |...| C2H5NO2 | DHMQDGOQFOQNFH-UHFFFAOYSA-N | DHMQDGOQFOQNFH | UHFFFAOYSA | N |
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323 +---+------------------+-----------------------------+------------------+------------+-------------+
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324 |...| C2H6OS | IAZDPXIOMUYVGZ-UHFFFAOYSA-N | IAZDPXIOMUYVGZ | UHFFFAOYSA | N |
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325 +---+------------------+-----------------------------+------------------+------------+-------------+
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326 |...| ... | ... | ... | ... | ... |
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327 +---+------------------+-----------------------------+------------------+------------+-------------+
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328
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329
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330
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331 **\2b. MetFragDatabaseType MetChem**
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332
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333 MetChem is a modified PubChem database and can be used in replace of PubChem
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334 for performing API calls to the public PubChem instance.
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335
1
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336 **\3. Database Search Relative Mass Deviation - ppm**
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337
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338 A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses.
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339
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340 **\4. Fragment Peak Match Relative Mass Deviation - ppm**
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341
1
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342 Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks.
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343
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344 **\5. Fragment Peak Match Absolute Mass Deviation (Da)**
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345
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346 Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks.
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347
1
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348 **\6. Polarity**
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349
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350 The polarity used for the mode of acquisition.
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351
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352 **\7. Schema**
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353
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354 The Schema used by the MSP file (e.g. generic MSP format or MassBank format)
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355
1
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356 **\8. Suspect list**
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357
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358 Choose whether to include a file containing a list of suspects.
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359
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360 **\9. MetFrag Score Types**
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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361
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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diff changeset
362 The type of scores MetFrac is using for the calculations. Please do not change the values unless you know what you are doing!
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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363
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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parents: 0
diff changeset
364 **\10. MetFrag Score Weights**
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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365
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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diff changeset
366 The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100%.
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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367
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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diff changeset
368 **\11. MetFrag Database Type**
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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369
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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diff changeset
370 Database to choose from.
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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371
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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372 **\12. minMSMSpeaks**
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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373
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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374 Minimum MS/MS peaks within a MS/MS spectra to be used for the MetFrag calculation
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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375
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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diff changeset
376 **\13. PreProcessFilter**
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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377
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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378 Various filters can be performed on the potential compounds prior to predicting the in silico spectra
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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379
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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diff changeset
380 **\14. PostProcessFilter**
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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381
4
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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diff changeset
382 To make the output more manageble results below certain criteria can be removed from the various filters can be
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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diff changeset
383 performed on the potential compounds prior to predicting the in silico spectra
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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diff changeset
384
9
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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385 Output
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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386 -------
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
387
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
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)
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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389
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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390 +-------------+--------------------------------------------+---+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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391 | adduct | name |...|
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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392 +-------------+--------------------------------------------+---+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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393 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
394 +-------------+--------------------------------------------+---+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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395 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
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diff changeset
396 +-------------+--------------------------------------------+---+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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397 | ... | ... |...|
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
398 +-------------+--------------------------------------------+---+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
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diff changeset
399
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
400 Table continued (these columns are derived from the MetFrag result):
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
parents: 8
diff changeset
401
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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402 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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403 |...| sample_name | ExplPeaks | FormulasOfExplPeaks | ... |
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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404 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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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- | ... |
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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406 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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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- | ... |
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
408 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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409 |...| ... | ... | ... | ... |
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
410 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
411
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
412
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
413 Table continued (columns are derived from the MetFrag result):
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
414
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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415 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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parents: 8
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416 |...| FragmenterScore | FragmenterScore_Values | FormulasOfExplPeaks | Identifier | InChI |...|
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
417 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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parents: 8
diff changeset
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 |...|
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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419 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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parents: 8
diff changeset
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 |...|
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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parents: 8
diff changeset
421 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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parents: 8
diff changeset
422 |...| ... | ... | ... | ... | ... |...|
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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parents: 8
diff changeset
423 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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parents: 8
diff changeset
424
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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parents: 8
diff changeset
425 Table continued (columns are derived from the MetFrag result):
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
426
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
427
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
428 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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429 |...| NoExplPeaks | NumberPeaksUsed | OfflineMetFusionScore | SMILES | Score | SuspectListScore | XlogP3 |
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
parents: 8
diff changeset
430 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
parents: 8
diff changeset
431 |...| 4 | 5 | 2.84566828424078 | C(C1C(C(C(C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
parents: 8
diff changeset
432 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
parents: 8
diff changeset
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 |
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
parents: 8
diff changeset
434 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
parents: 8
diff changeset
435 |...| ... | ... | ... | ... | ... | ... | ... |
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
parents: 8
diff changeset
436 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
tomnl
parents: 8
diff changeset
437
5763234618d4 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
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diff changeset
438
4
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
tomnl
parents: 3
diff changeset
439 Additional notes
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
tomnl
parents: 3
diff changeset
440 --------------------
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
tomnl
parents: 3
diff changeset
441
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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parents: 3
diff changeset
442 The following adducts (and format) are currently supported in the MSP file. The neutral mass is automatically
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
tomnl
parents: 3
diff changeset
443 calculated for the precursor m/z by subtracting the adduct mass
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
444
4
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
tomnl
parents: 3
diff changeset
445 - '[M+H]+': 1.007276,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
tomnl
parents: 3
diff changeset
446 - '[M+NH4]+': 18.034374,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
tomnl
parents: 3
diff changeset
447 - '[M+Na]+': 22.989218,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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parents: 3
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448 - '[M+K]+': 38.963158,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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449 - '[M+CH3OH+H]+': 33.033489,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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450 - '[M+ACN+H]+': 42.033823,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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451 - '[M+ACN+Na]+': 64.015765,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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452 - '[M+2ACN+H]+': 83.06037,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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parents: 3
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453 - '[M-H]-': -1.007276,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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454 - '[M+Cl]-': 34.969402,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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455 - '[M+HCOO]-': 44.99819,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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parents: 3
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456 - '[M-H+HCOOH]-': 44.99819,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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457 - '[M+CH3COO]-': 59.01385,
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
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458 - '[M-H+CH3COOH]-': 59.01385
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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459
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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460 Developers and contributors
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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461 ---------------------------
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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462 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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parents: 0
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463 - **Julien Saint-Vanne (julien.saint-vanne@sb-roscoff.fr) - ABiMS (France)**
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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464 - **Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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465 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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466 - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)**
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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467 - **Payam Emami (payam.emami@medsci.uu.se) - Uppsala Universitet (Sweden)**
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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468 - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)**
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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469 </help>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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470 <citations>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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471 <citation type="doi">10.1186/s13321-016-0115-9</citation>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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472 </citations>
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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473 </tool>