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annotate metfrag.xml @ 4:eb581a101672 draft

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planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
author tomnl
date Thu, 01 Aug 2019 09:02:47 -0400
parents 5ee936e570a7
children c53ed894d736
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1 <tool id="metfrag" name="MetFrag" version="2.4.2+galaxy0.1.9">
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>
4
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6 <stdio>
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7 <regex match="Cannot allocate memory"
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8 source="stderr"
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9 level="fatal_oom"
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10 description="Out of memory error occurred" />
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11 </stdio>
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12 <command detect_errors="exit_code">
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13 <![CDATA[
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15 python $__tool_directory__/metfrag.py
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16 --input_pth "$input"
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17 --result_pth '$results'
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18 --temp_dir './temp/'
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20 --cores_top_level \${GALAXY_SLOTS:-4}
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22 --MetFragDatabaseType '$db_select.MetFragDatabaseType'
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24 #if $db_select.MetFragDatabaseType == "LocalCSV":
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25 --LocalDatabasePath '$db_select.LocalDatabasePath'
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26 #elif $db_select.MetFragDatabaseType == "MetChem":
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27 --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp'
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28 #end if
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29
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30 --DatabaseSearchRelativeMassDeviation $DatabaseSearchRelativeMassDeviation
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31 --FragmentPeakMatchRelativeMassDeviation $FragmentPeakMatchRelativeMassDeviation
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32 --FragmentPeakMatchAbsoluteMassDeviation $FragmentPeakMatchAbsoluteMassDeviation
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33 --polarity '$polarity'
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34
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35 --MetFragScoreTypes '$suspectlist.MetFragScoreTypes'
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36 --MetFragScoreWeights '$suspectlist.MetFragScoreWeights'
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37
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38 #if $suspectlist.suspectselector == 'includesuspects':
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39 #if $suspectlist.includesuspects_default_cond:
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40 --ScoreSuspectLists '$__tool_directory__/test-data/UNPD_DB.inchikeys.txt'
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41 #else
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42 --ScoreSuspectLists '$suspectlist.includesuspects_custom_cond.ScoreSuspectLists'
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43 #end if
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44 #end if
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45
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46 --meta_select_col $meta_select_col
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47 --minMSMSpeaks $minMSMSpeaks
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48 --schema $schema
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49
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50 $PreProcessFilter.UnconnectedCompoundFilter
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51 $PreProcessFilter.IsotopeFilter
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52
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53
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54 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements'
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55 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements'
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56 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList'
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57 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList'
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58 --FilterIncludedElements '$PreProcessFilter.FilterIncludedElements'
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59 --FilterExcludedElements '$PreProcessFilter.FilterExcludedElements'
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60 --FilterIncludedExclusiveElements '$PreProcessFilter.FilterIncludedExclusiveElements'
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61
4
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62 $skip_invalid_adducts
1
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63 --score_thrshld $PostProcessFilter.score_thrshld
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64 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld
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65
0
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66 ]]></command>
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67 <inputs>
1
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68
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69 <param name="input" type="data" format="msp,txt" label="MSP file (Output from Create MSP tool)"/>
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70 <conditional name="db_select">
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71 <param name="MetFragDatabaseType" type="select" label="Choose Compound Database"
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72 argument="--MetFragDatabaseType">
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73 <option value="PubChem" selected="true">PubChem</option>
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74 <option value="KEGG">KEGG</option>
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75 <option value="LocalCSV">Local database (csv)</option>
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76 <option value="MetChem">MetChem</option>
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77 </param>
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78 <when value="MetChem">
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79 <param name="LocalMetChemDatabaseServerIp" type="text" label="MetChem URL"
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80 argument="--LocalMetChemDatabaseServerIp" />
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81 </when>
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82 <when value="LocalCSV">
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83 <param name="LocalDatabasePath" type="data" format="csv" label="Local database of compounds (CSV format)" argument="--LocalDatabasePath"/>
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84 </when>
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85 <when value="KEGG">
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86 </when>
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87 <when value="PubChem">
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88 </when>
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89 </conditional>
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90 <param name="DatabaseSearchRelativeMassDeviation" type="float" value="10"
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91 label="Relative Mass Deviation for database search (ppm)" argument="--DatabaseSearchRelativeMassDeviation"
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92 help="A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses"/>
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93 <param name="FragmentPeakMatchRelativeMassDeviation" type="float" value="5"
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94 label="Fragment Peak Match Relative Mass Deviation (ppm)" argument="--FragmentPeakMatchRelativeMassDeviation"
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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 name="FragmentPeakMatchAbsoluteMassDeviation" type="float" value="0.001"
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97 label="Fragment Peak Match Absolute Mass Deviation (Da)" argument="FragmentPeakMatchAbsoluteMassDeviation"
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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 name="polarity" type="select" label="Polarity" help="The polarity used for the mode of acquisition">
0
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100 <option value="pos" selected="true">Positive</option>
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101 <option value="neg">Negative</option>
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102 </param>
1
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103 <param name="schema" type="select" label="Schema"
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104 help="The schema used for the MSP file (auto will try automatically determine the schema)">
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105 <option value="auto" selected="True">Auto</option>
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106 <option value="msp" >Generic MSP</option>
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107 <option value="massbank">MassBank</option>
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108 </param>
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109 <param name="meta_select_col" type="select" label="Choose how additional metadata columns are extracted"
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110 help="The MetFrag output can have additional meta data columns added, these can be either extracted
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111 from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns
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112 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and :
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113 e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns">
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114 <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option>
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115 <option value="name_split" >Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option>
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116 <option value="all">Extra metadata columns from all MSP parameters</option>
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117 </param>
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118
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119 <conditional name="suspectlist">
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120 <param name="suspectselector" type="select" optional="False" label="Suspect list" help="Choose whether to include a suspect list">
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121 <option value="includesuspects" >Include suspect list</option>
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122 <option value="excludesuspects" selected="True">Do not include suspect list</option>
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123 </param>
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124 <when value="includesuspects">
4
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125 <conditional name="includesuspects_default_cond">
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126 <param name="includesuspects_default_bool" type="boolean" label="Use default list of suspect compounds?"
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127 help="Either provide a file containing a list of suspect compounds or a default file
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128 of of an aggregated list of in silico predicted MS/MS spectra of natural products
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129 from the Universal Natural Products Database (http://pkuxxj.pku.edu.cn/UNPD/index.php).
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130 The list is an aggregated version of the github repository https://github.com/oolonek/ISDB/tree/master/Data/dbs."/>
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131 <when value="true">
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132 <param name="ScoreSuspectLists" type="data" format="txt" optional="False" label="Suspect list file"
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133 help="File containing a list of suspects inchikeys" />
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134 </when>
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135 <when value="false">
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136 </when>
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137 </conditional>
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138
1
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139 <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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140 <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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141 </when>
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142 <when value="excludesuspects">
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143 <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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144 <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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145 </when>
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146 </conditional>
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147
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148 <param name="minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/>
4
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149 <param name="skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?"
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150 truevalue="--skip_invalid_adducts" falsevalue=""
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151 help="If no adduct type is provided within the MSP file or if the adduct type is not usable
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152 with MetFrag, set to true if these spectra should be skipped or false if the default
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153 of [M+H]+ for pos data or [M-H]- for neg data should be used"/>
1
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154 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False">
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155 <param name="UnconnectedCompoundFilter" type="boolean" checked="false" truevalue="--UnconnectedCompoundFilter"
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156 falsevalue="" label="filter non-connected compounds (e.g. salts)" help=""/>
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157 <param name="IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter" falsevalue=""
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158 label="filter compounds containing non-standard isotopes" help=""/>
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159 <param name="FilterMinimumElements" type="text" label="Minimum Elements Filter"
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160 help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least 2 nitrogens and 3 oxygens"/>
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161 <param name="FilterMaximumElements" type="text" label="Maximum Elements Filter"
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162 help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at maximum 5 nitrogens and 7 oxygens"/>
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163 <param name="FilterSmartsInclusionList" type="text" label="Include substructures"
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164 help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds containing benzene"/>
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165 <param name="FilterSmartsExclusionList" type="text" label="Exclude substructures"
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166 help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds containing hydroxyl groups"/>
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167 <param name="FilterIncludedElements" type="text" label="Include elements"
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168 help="Filter by presence of defined elements (other elements are allowed). Ex: 'N,O' include compounds containing nitrogen and oxygen" />
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169 <param name="FilterIncludedExclusiveElements" type="text" label="Include elements (exclusive)"
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170 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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171 <param name="FilterExcludedElements" type="text" label="Exclude elements"
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172 help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out compounds including bromine or chlorine"/>
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173 </section>
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174
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175 <section name="PostProcessFilter" title="PostProcessing filters" expanded="False">
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176 <param name="score_thrshld" type="float" label="Threshold for score after MetFrag search" max="1" min="0" value="0"/>
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177 <param name="pctexplpeak_thrshld" type="float" label="Minimum percentage of explain peaks" max="100" min="0" value="0"/>
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178 </section>
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179
0
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180 </inputs>
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181 <outputs>
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182 <data name="results" format="tabular" label="${tool.name} results of ${input.name}" />
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183 </outputs>
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184 <tests>
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185 <test>
4
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186 <!-- Test "massbank" style data format -->
1
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187 <param name="input" value="massbank_format.txt"/>
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188 <param name="schema" value="massbank"/>
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189 <param name="MetFragDatabaseType" value="LocalCSV"/>
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190 <param name="LocalDatabasePath" value="demo_db.csv"/>
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191 <output name="results" file="metfrag_massbank.tabular"/>
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192 </test>
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193 <test>
4
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194 <!-- Test "generic" style data format -->
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195 <param name="input" value="generic_format.msp"/>
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196 <param name="schema" value="msp"/>
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197 <param name="MetFragDatabaseType" value="LocalCSV"/>
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198 <param name="LocalDatabasePath" value="demo_db.csv"/>
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199 <output name="results" file="metfrag_msp.tabular"/>
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200 </test>
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201 <test>
4
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202 <!-- Test PubChem API with "winter" dataset -->
1
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203 <param name="input" value="winter_pos.msp"/>
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204 <param name="PostProcessFilter|score_thrshld" value="0.9"/>
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205 <param name="MetFragDatabaseType" value="PubChem"/>
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206 <output name="results" file="winter_pos.tabular"/>
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207 </test>
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208 <test>
4
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209 <!-- Test actual MassBank data for Glucose -->
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210 <param name="input" value="RP022611.txt"/>
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211 <param name="MetFragDatabaseType" value="LocalCSV"/>
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212 <param name="LocalDatabasePath" value="demo_db.csv"/>
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213 <output name="results" file="RP022611.tabular"/>
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214 </test>
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215 <test>
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216 <!-- Test actual MassBank data for Glucose (all metadata columns in output-->
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217 <param name="input" value="RP022611.txt"/>
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218 <param name="schema" value="massbank"/>
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219 <param name="MetFragDatabaseType" value="LocalCSV"/>
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220 <param name="LocalDatabasePath" value="demo_db.csv"/>
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221 <param name="meta_select_col" value="all"/>
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222 <output name="results" file="RP022611_all_col.tabular"/>
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223 </test>
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224 <test>
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225 <!-- Test actual MassBank data for Glucose (include suspect list - default)-->
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226 <param name="input" value="RP022611.txt"/>
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227 <param name="schema" value="massbank"/>
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228 <param name="suspectlist|suspectselector" value="includesuspects"/>
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229 <param name="suspectlist|includesuspects_default_cond|includesuspects_default_bool" value="true"/>
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230 <param name="suspectlist|MetFragScoreTypes" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore"/>
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231 <param name="suspectlist|MetFragScoreWeights" value="0.4,0.6,1.0"/>
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232 <output name="results" file="RP022611_suspect_default.txt"/>
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233 </test>
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234 <test>
4
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235 <!-- Test actual MassBank data for Glucose (include suspect list - custom)-->
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236 <param name="input" value="RP022611.txt"/>
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237 <param name="schema" value="massbank"/>
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238 <param name="suspectlist|suspectselector" value="includesuspects"/>
4
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239 <param name="suspectlist|includesuspects_default_cond|includesuspects_default_bool" value="false"/>
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240 <param name="suspectlist|includesuspects_default_cond|ScoreSuspectLists" value="UNPD_DB.inchikeys.txt"/>
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241 <param name="suspectlist|MetFragScoreTypes" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore"/>
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242 <param name="suspectlist|MetFragScoreWeights" value="0.4,0.6,1.0"/>
4
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243 <output name="results" file="RP022611_suspect_default.txt"/>
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244 </test>
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245 <test>
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246 <!-- Test actual MassBank data for Glucose (include suspect list - custom)-->
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247 <param name="input" value="invalid_adduct.msp"/>
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248 <param name="skip_invalid_adducts" value="true"/>
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249 <output name="results" file="invalid_adduct_result.txt"/>
0
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250 </test>
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251 </tests>
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252 <help>
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253 -------
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254 MetFrag
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255 -------
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256
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257 Description
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258 -----------
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259
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260 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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261
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262 Website: http://c-ruttkies.github.io/MetFrag
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263
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264 Parameters
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265 ----------
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266
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267 **\1. MSP file**
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268
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269 MSP file created using *Create MSP* tool
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270
1
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271 **\2a. MetFragDatabaseType (public databases)**
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272
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273 * PubChem
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274
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275 * KEGG
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276
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277
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278 **\2b. MetFragDatabaseType (local CSV file database)**
0
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279
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280 Custom database file in CSV format with the following structure:
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281
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282 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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283 | Identifier | MonoisotopicMass | SMILES | InChI | Name |...|
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284 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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285 | HMDB0000123 | 75.03202841 | NCC(O)=O | InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) | Glycine |...|
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286 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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287 | HMDB0002151 | 78.0139355 | CS(C)=O | InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 | Dimethyl sulfoxide |...|
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288 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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289 | ... | ... | ... | ... | ... |...|
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290 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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291
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292
1
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293 Table continued:
0
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294
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295 +---+------------------+-----------------------------+------------------+------------+-------------+
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296 |...| MolecularFormula | InChIKey | InChIKey1 | InChIKey2 | InChIKey3 |
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297 +---+------------------+-----------------------------+------------------+------------+-------------+
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298 |...| C2H5NO2 | DHMQDGOQFOQNFH-UHFFFAOYSA-N | DHMQDGOQFOQNFH | UHFFFAOYSA | N |
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299 +---+------------------+-----------------------------+------------------+------------+-------------+
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300 |...| C2H6OS | IAZDPXIOMUYVGZ-UHFFFAOYSA-N | IAZDPXIOMUYVGZ | UHFFFAOYSA | N |
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301 +---+------------------+-----------------------------+------------------+------------+-------------+
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302 |...| ... | ... | ... | ... | ... |
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303 +---+------------------+-----------------------------+------------------+------------+-------------+
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304
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305
1
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306 **\2b. MetFragDatabaseType MetChem local database**
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307
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308 MetChem is a modified PubChem database and can be used in replace of PubChem
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309 for performing API calls to the public PubChem instance. Details regarding how to serve the database can be located
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310 here:
0
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311
1
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312 **\3. Database Search Relative Mass Deviation - ppm**
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313
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314 A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses.
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315
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316 **\4. Fragment Peak Match Relative Mass Deviation - ppm**
0
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317
1
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318 Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks.
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319
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320 **\5. Fragment Peak Match Absolute Mass Deviation (Da)**
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321
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322 Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks.
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323
1
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324 **\6. Polarity**
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325
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326 The polarity used for the mode of acquisition.
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327
1
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328 **\7. Schema**
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329
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330 The Schema used by the MSP file (e.g. generic MSP format or MassBank format)
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331
1
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332 **\8. Suspect list**
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333
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334 Choose whether to include a file containing a list of suspects.
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335
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336 **\9. MetFrag Score Types**
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337
1
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338 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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339
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340 **\10. MetFrag Score Weights**
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341
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342 The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100%.
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343
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344 **\11. MetFrag Database Type**
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345
1
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346 Database to choose from.
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347
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348 **\12. minMSMSpeaks**
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349
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350 Minimum MS/MS peaks within a MS/MS spectra to be used for the MetFrag calculation
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351
1
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352 **\13. PreProcessFilter**
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353
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354 Various filters can be performed on the potential compounds prior to predicting the in silico spectra
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355
1
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356 **\14. PostProcessFilter**
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357
4
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358 To make the output more manageble results below certain criteria can be removed from the various filters can be
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359 performed on the potential compounds prior to predicting the in silico spectra
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360
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361 Additional notes
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362 --------------------
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363
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364 The following adducts (and format) are currently supported in the MSP file. The neutral mass is automatically
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365 calculated for the precursor m/z by subtracting the adduct mass
0
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366
4
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367 - '[M+H]+': 1.007276,
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368 - '[M+NH4]+': 18.034374,
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369 - '[M+Na]+': 22.989218,
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370 - '[M+K]+': 38.963158,
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371 - '[M+CH3OH+H]+': 33.033489,
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372 - '[M+ACN+H]+': 42.033823,
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373 - '[M+ACN+Na]+': 64.015765,
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374 - '[M+2ACN+H]+': 83.06037,
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375 - '[M-H]-': -1.007276,
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376 - '[M+Cl]-': 34.969402,
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377 - '[M+HCOO]-': 44.99819,
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378 - '[M-H+HCOOH]-': 44.99819,
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379 - '[M+CH3COO]-': 59.01385,
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380 - '[M-H+CH3COOH]-': 59.01385
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381
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382 Developers and contributors
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383 ---------------------------
1
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384 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
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385 - **Julien Saint-Vanne (julien.saint-vanne@sb-roscoff.fr) - ABiMS (France)**
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386 - **Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
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387 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
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388 - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)**
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389 - **Payam Emami (payam.emami@medsci.uu.se) - Uppsala Universitet (Sweden)**
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390 - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)**
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391
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392
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393 </help>
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394 <citations>
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395 <citation type="doi">10.1186/s13321-016-0115-9</citation>
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396 </citations>
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397 </tool>