annotate metfrag.xml @ 0:fd5c0b39569a draft

"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
author computational-metabolomics
date Wed, 05 Feb 2020 12:30:06 -0500
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children 9ee2e2ceb2c9
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fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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1 <tool id="metfrag" name="MetFrag" version="2.4.5+galaxy1">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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2 <description>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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3 in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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4 </description>
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5 <macros>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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6 <import>macros.xml</import>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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7 </macros>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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8 <requirements>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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9 <requirement type="package" version="2.4.5">metfrag</requirement>
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10 </requirements>
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11 <stdio>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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12 <regex match="Cannot allocate memory"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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13 source="stderr"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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14 level="fatal_oom"
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15 description="Out of memory error occurred" />
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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16 </stdio>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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17 <command detect_errors="exit_code">
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18 <![CDATA[
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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19 python '$__tool_directory__/metfrag.py'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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20 --input_pth '$input'
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21 --result_pth '$results'
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22 --temp_dir './temp/'
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23
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24 --cores_top_level \${GALAXY_SLOTS:-4}
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25
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26 --MetFragDatabaseType '$db_select.MetFragDatabaseType'
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27
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28 #if $db_select.MetFragDatabaseType == 'LocalCSV':
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29 --LocalDatabasePath '$db_select.LocalDatabasePath'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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30 #elif $db_select.MetFragDatabaseType == 'MetChem':
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31 --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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32 #end if
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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33
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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34 --DatabaseSearchRelativeMassDeviation $DatabaseSearchRelativeMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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35 --FragmentPeakMatchRelativeMassDeviation $FragmentPeakMatchRelativeMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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36 --FragmentPeakMatchAbsoluteMassDeviation $FragmentPeakMatchAbsoluteMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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37 --polarity '$polarity'
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38
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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39 --MetFragScoreTypes '$suspectlist.MetFragScoreTypes'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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40 --MetFragScoreWeights '$suspectlist.MetFragScoreWeights'
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41
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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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'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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45 #else
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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46 --ScoreSuspectLists '$suspectlist.includesuspects_custom_cond.ScoreSuspectLists'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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47 #end if
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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48 #end if
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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>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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89 <param argument="--DatabaseSearchRelativeMassDeviation" type="float" min="0" value="10"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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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"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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93 <param argument="--FragmentPeakMatchRelativeMassDeviation" type="float" min="0" value="5"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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94 label="Fragment Peak Match Relative Mass Deviation (ppm)"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
95 help="Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks" />
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
96 <param argument="--FragmentPeakMatchAbsoluteMassDeviation" type="float" min="0" value="0.001"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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97 label="Fragment Peak Match Absolute Mass Deviation (Da)"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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98 help="Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks" />
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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99 <param argument="--polarity" type="select" label="Polarity"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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100 help="The polarity used for the mode of acquisition">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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101 <option value="pos" selected="true">Positive</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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102 <option value="neg">Negative</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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103 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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104 <param argument="--schema" type="select" label="Schema"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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105 help="The schema used for the MSP file (auto will try automatically determine the schema)">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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106 <option value="auto" selected="True">Auto</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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107 <option value="msp">Generic MSP</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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108 <option value="massbank">MassBank</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
diff changeset
109 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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110 <param argument="--meta_select_col" type="select"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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111 label="Choose how additional metadata columns are extracted"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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112 help="The MetFrag output can have additional meta data columns added, these can be either extracted
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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113 from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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114 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and :
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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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">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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116 <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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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>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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118 <option value="all">Extra metadata columns from all MSP parameters</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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119 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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120 <conditional name="suspectlist">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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121 <param name="suspectselector" type="select" label="Suspect list"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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122 help="Choose whether to include a suspect list">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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123 <option value="includesuspects" >Include suspect list</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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124 <option value="excludesuspects" selected="True">Do not include suspect list</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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125 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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126 <when value="includesuspects">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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127 <conditional name="includesuspects_default_cond">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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128 <param name="includesuspects_default_bool" type="boolean"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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129 label="Use default list of suspect compounds?"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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130 help="Either provide a file containing a list of suspect compounds or a default file
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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131 of an aggregated list of in silico predicted MS/MS spectra of natural products
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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132 from the Universal Natural Products Database (http://pkuxxj.pku.edu.cn/UNPD/index.php).
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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133 The list is an aggregated version of the github repository https://github.com/oolonek/ISDB/tree/master/Data/dbs."/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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134 <when value="true"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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135 <when value="false">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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136 <param argument="--ScoreSuspectLists" type="data" format="txt" optional="True"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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137 label="Suspect list file" help="File containing a list of suspects inchikeys" />
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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138 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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139 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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140 <expand macro="metfrag_scoring"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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parents:
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141 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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142 <when value="excludesuspects">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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143 <expand macro="metfrag_scoring" suspectlistscore="False" weights="1.0,1.0"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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144 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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145 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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146 <param argument="--minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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147 <param argument="--skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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148 truevalue="--skip_invalid_adducts" falsevalue="" checked="true"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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149 help="If no adduct type is provided within the MSP file or if the adduct type is not usable
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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150 with MetFrag, set to 'yes' if these spectra should be skipped or 'no' if the default
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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151 of [M+H]+ for pos data or [M-H]- for neg data should be used"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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152 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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153 <param argument="--UnconnectedCompoundFilter" type="boolean" checked="false"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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154 truevalue="--UnconnectedCompoundFilter" falsevalue=""
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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155 label="filter non-connected compounds (e.g. salts)" help=""/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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156 <param argument="--IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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157 falsevalue="" label="filter compounds containing non-standard isotopes" help=""/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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158 <param argument="--FilterMinimumElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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159 optional="true" label="Minimum Elements Filter"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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160 help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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161 2 nitrogens and 3 oxygens">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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162 <expand macro="text-alphanumeric-regex-validator"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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163 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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164 <param argument="--FilterMaximumElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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165 optional="true" label="Maximum Elements Filter"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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166 help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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167 maximum 5 nitrogens and 7 oxygens">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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168 <expand macro="text-alphanumeric-regex-validator"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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169 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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170 <param argument="--FilterSmartsInclusionList" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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171 optional="true" label="Include substructures"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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172 help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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173 containing benzene"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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174 <param argument="--FilterSmartsExclusionList" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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175 optional="true" label="Exclude substructures"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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176 help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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177 containing hydroxyl groups"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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178 <param argument="--FilterIncludedElements" type="text"
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179 optional="true" label="Include elements"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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180 help="Filter by presence of defined elements (other elements are allowed).
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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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"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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183 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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184 <param argument="--FilterIncludedExclusiveElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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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" >
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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188 <expand macro="text-alphanumeric-comma-regex-validator"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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189 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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190 <param argument="--FilterExcludedElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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191 optional="true" label="Exclude elements"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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192 help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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193 compounds including bromine or chlorine">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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194 <expand macro="text-alphanumeric-comma-regex-validator"/>
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195 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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196 </section>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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197 <section name="PostProcessFilter" title="PostProcessing filters" expanded="False">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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198 <param argument="--score_thrshld" type="float" label="Threshold for score after MetFrag search"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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199 max="1" min="0" value="0"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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200 <param argument="--pctexplpeak_thrshld" type="float" label="Minimum percentage of explain peaks"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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201 max="100" min="0" value="0"/>
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202 </section>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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203 </inputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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204 <outputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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205 <data name="results" format="tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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206 </outputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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207 <tests>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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208 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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209 <!-- Test "massbank" style data format -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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210 <param name="input" value="massbank_format.txt"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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211 <param name="schema" value="massbank"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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212 <param name="skip_invalid_adducts" value="false"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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213 <param name="MetFragDatabaseType" value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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214 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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215 <param name="LocalDatabasePath" value="demo_db.csv"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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216 <output name="results" file="metfrag_massbank.tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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217 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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218 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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219 <!-- Test "generic" style data format -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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220 <param name="input" value="generic_format.msp"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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221 <param name="schema" value="msp"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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222 <param name="MetFragDatabaseType" value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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223 <param name="skip_invalid_adducts" value="false"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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224 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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225 <param name="LocalDatabasePath" value="demo_db.csv"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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226 <output name="results" file="metfrag_msp.tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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227 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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228 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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229 <!-- Test PubChem API with "winter" dataset -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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230 <param name="input" value="winter_pos.msp"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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231 <section name="PostProcessFilter">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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232 <param name="score_thrshld" value="0.9"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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233 </section>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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234 <param name="MetFragDatabaseType" value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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235 <output name="results" file="winter_pos.tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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236 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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237 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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238 <!-- Test actual MassBank data for Glucose -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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239 <param name="input" value="RP022611.txt"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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240 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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241 <param name="LocalDatabasePath" value="demo_db.csv"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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242 <output name="results" file="RP022611.tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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243 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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244 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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245 <!-- Test actual MassBank data for Glucose (all metadata columns in output-->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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246 <param name="input" value="RP022611.txt"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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247 <param name="schema" value="massbank"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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248 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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249 <param name="LocalDatabasePath" value="demo_db.csv"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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250 <param name="meta_select_col" value="all"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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251 <output name="results" file="RP022611_all_col.tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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252 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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253 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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254 <!-- Test actual MassBank data for Glucose (include suspect list - default)-->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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255 <param name="input" value="RP022611.txt"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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256 <param name="schema" value="massbank"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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257 <conditional name="suspectlist">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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258 <param name="suspectselector" value="includesuspects"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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259 <conditional name="includesuspects_default_cond">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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260 <param name="includesuspects_default_bool" value="true"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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261 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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262 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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263 <output name="results" file="RP022611_suspect_default.txt"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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264 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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265 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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266 <!-- Test invalid adduct -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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267 <param name="input" value="invalid_adduct.msp"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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268 <param name="skip_invalid_adducts" value="true"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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269 <output name="results" file="invalid_adduct_result.txt" ftype="tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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270 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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271 </tests>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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272 <help>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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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
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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
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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
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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
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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
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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
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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
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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**
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361
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362 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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363
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364 **\10. MetFrag Score Weights**
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365
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366 The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100%.
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367
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368 **\11. MetFrag Database Type**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
369
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
370 Database to choose from.
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
371
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
372 **\12. minMSMSpeaks**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
373
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
374 Minimum MS/MS peaks within a MS/MS spectra to be used for the MetFrag calculation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
375
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
376 **\13. PreProcessFilter**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
377
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
378 Various filters can be performed on the potential compounds prior to predicting the in silico spectra
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
379
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
380 **\14. PostProcessFilter**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
381
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
382 To make the output more manageble results below certain criteria can be removed from the various filters can be
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
383 performed on the potential compounds prior to predicting the in silico spectra
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
384
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
385 Output
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
386 -------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
387
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
389
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
390 +-------------+--------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
391 | adduct | name |...|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
392 +-------------+--------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
393 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
394 +-------------+--------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
395 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
396 +-------------+--------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
397 | ... | ... |...|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
398 +-------------+--------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
399
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
400 Table continued (these columns are derived from the MetFrag result):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
401
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
402 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
403 |...| sample_name | ExplPeaks | FormulasOfExplPeaks | ... |
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
404 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
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- | ... |
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
406 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
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- | ... |
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
408 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
409 |...| ... | ... | ... | ... |
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
410 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
411
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
412
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
413 Table continued (columns are derived from the MetFrag result):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
414
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
415 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
416 |...| FragmenterScore | FragmenterScore_Values | FormulasOfExplPeaks | Identifier | InChI |...|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
417 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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 |...|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
419 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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 |...|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
421 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
422 |...| ... | ... | ... | ... | ... |...|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
423 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
424
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
425 Table continued (columns are derived from the MetFrag result):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
426
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
427
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
428 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
429 |...| NoExplPeaks | NumberPeaksUsed | OfflineMetFusionScore | SMILES | Score | SuspectListScore | XlogP3 |
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
430 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
431 |...| 4 | 5 | 2.84566828424078 | C(C1C(C(C(C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
432 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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 |
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
434 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
435 |...| ... | ... | ... | ... | ... | ... | ... |
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
436 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
437
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
438
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
439 Additional notes
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
440 --------------------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
441
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
442 The following adducts (and format) are currently supported in the MSP file. The neutral mass is automatically
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
443 calculated for the precursor m/z by subtracting the adduct mass
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
444
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
445 - '[M+H]+': 1.007276,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
446 - '[M+NH4]+': 18.034374,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
447 - '[M+Na]+': 22.989218,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
448 - '[M+K]+': 38.963158,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
449 - '[M+CH3OH+H]+': 33.033489,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
450 - '[M+ACN+H]+': 42.033823,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
451 - '[M+ACN+Na]+': 64.015765,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
452 - '[M+2ACN+H]+': 83.06037,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
453 - '[M-H]-': -1.007276,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
454 - '[M+Cl]-': 34.969402,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff changeset
455 - '[M+HCOO]-': 44.99819,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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456 - '[M-H+HCOOH]-': 44.99819,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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457 - '[M+CH3COO]-': 59.01385,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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458 - '[M-H+CH3COOH]-': 59.01385
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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459
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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460 Developers and contributors
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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461 ---------------------------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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462 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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463 - **Julien Saint-Vanne (julien.saint-vanne@sb-roscoff.fr) - ABiMS (France)**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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464 - **Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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465 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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466 - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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467 - **Payam Emami (payam.emami@medsci.uu.se) - Uppsala Universitet (Sweden)**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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468 - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)**
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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469 </help>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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470 <citations>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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471 <citation type="doi">10.1186/s13321-016-0115-9</citation>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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472 </citations>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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473 </tool>