metfrag: metfrag.xml annotate

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
parents
children	9ee2e2ceb2c9

rev	line source
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	2 <description>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	4 </description>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	5 <macros>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	6 <import>macros.xml</import>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	7 </macros>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	8 <requirements>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	9 <requirement type="package" version="2.4.5">metfrag</requirement>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	10 </requirements>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	11 <stdio>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	12 <regex match="Cannot allocate memory"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	13 source="stderr"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	14 level="fatal_oom"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	15 description="Out of memory error occurred" />
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	16 </stdio>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	17 <command detect_errors="exit_code">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	18 <![CDATA[
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	19 python '$__tool_directory__/metfrag.py'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	20 --input_pth '$input'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	21 --result_pth '$results'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	22 --temp_dir './temp/'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	23
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	24 --cores_top_level \${GALAXY_SLOTS:-4}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	25
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	26 --MetFragDatabaseType '$db_select.MetFragDatabaseType'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	27
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	28 #if $db_select.MetFragDatabaseType == 'LocalCSV':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	29 --LocalDatabasePath '$db_select.LocalDatabasePath'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	30 #elif $db_select.MetFragDatabaseType == 'MetChem':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	31 --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	32 #end if
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	33
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	34 --DatabaseSearchRelativeMassDeviation $DatabaseSearchRelativeMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	35 --FragmentPeakMatchRelativeMassDeviation $FragmentPeakMatchRelativeMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	36 --FragmentPeakMatchAbsoluteMassDeviation $FragmentPeakMatchAbsoluteMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	37 --polarity '$polarity'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	38
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	39 --MetFragScoreTypes '$suspectlist.MetFragScoreTypes'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	40 --MetFragScoreWeights '$suspectlist.MetFragScoreWeights'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	41
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	42 #if $suspectlist.suspectselector == 'includesuspects':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	43 #if $suspectlist.includesuspects_default_cond:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	44 --ScoreSuspectLists '$__tool_directory__/UNPD_DB.inchikeys.txt'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	45 #else
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	46 --ScoreSuspectLists '$suspectlist.includesuspects_custom_cond.ScoreSuspectLists'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	47 #end if
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	48 #end if
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	49
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	50 --meta_select_col $meta_select_col
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	51 --minMSMSpeaks $minMSMSpeaks
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	52 --schema $schema
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	53
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	54 $PreProcessFilter.UnconnectedCompoundFilter
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	55 $PreProcessFilter.IsotopeFilter
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	56
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	57 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	58 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	59 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	60 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	61 --FilterIncludedElements '$PreProcessFilter.FilterIncludedElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	62 --FilterExcludedElements '$PreProcessFilter.FilterExcludedElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	63 --FilterIncludedExclusiveElements '$PreProcessFilter.FilterIncludedExclusiveElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	64
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	65 $skip_invalid_adducts
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	66 --score_thrshld $PostProcessFilter.score_thrshld
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	67 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	68
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	69 ]]></command>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	70 <inputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	71 <param name="input" type="data" format="msp" label="MSP file (Output from Create MSP tool)"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	72 <conditional name="db_select">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	73 <param argument="--MetFragDatabaseType" type="select" label="Choose Compound Database">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	74 <option value="PubChem" selected="true">PubChem</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	75 <option value="KEGG">KEGG</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	76 <option value="LocalCSV">Local database (csv)</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	77 <option value="MetChem">MetChem</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	78 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	79 <when value="MetChem">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	80 <param argument="--LocalMetChemDatabaseServerIp" type="text" label="MetChem URL"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	81 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	82 <when value="LocalCSV">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	83 <param argument="--LocalDatabasePath" type="data" format="csv"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	84 label="Local database of compounds (CSV format)" />
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	85 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	86 <when value="KEGG"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	87 <when value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	88 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	89 <param argument="--DatabaseSearchRelativeMassDeviation" type="float" min="0" value="10"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	90 label="Relative Mass Deviation for database search (ppm)"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	91 help="A value in ppm that defines the deviation of theoretical masses in the database
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	92 vs. the measured masses"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	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" computational-metabolomics parents: diff changeset	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: diff changeset	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: diff changeset	101 <option value="pos" selected="true">Positive</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	102 <option value="neg">Negative</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	103 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	104 <param argument="--schema" type="select" label="Schema"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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: diff changeset	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: diff changeset	107 <option value="msp">Generic MSP</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	108 <option value="massbank">MassBank</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	109 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	110 <param argument="--meta_select_col" type="select"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	111 label="Choose how additional metadata columns are extracted"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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: diff changeset	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: diff changeset	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: diff changeset	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 parents: diff changeset	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" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	119 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	120 <conditional name="suspectlist">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	121 <param name="suspectselector" type="select" label="Suspect list"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	122 help="Choose whether to include a suspect list">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	123 <option value="includesuspects" >Include suspect list</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	125 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	126 <when value="includesuspects">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	127 <conditional name="includesuspects_default_cond">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	128 <param name="includesuspects_default_bool" type="boolean"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	129 label="Use default list of suspect compounds?"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	134 <when value="true"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	135 <when value="false">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	136 <param argument="--ScoreSuspectLists" type="data" format="txt" optional="True"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	138 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	139 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	140 <expand macro="metfrag_scoring"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	141 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	142 <when value="excludesuspects">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	144 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	145 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	148 truevalue="--skip_invalid_adducts" falsevalue="" checked="true"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	152 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	153 <param argument="--UnconnectedCompoundFilter" type="boolean" checked="false"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	154 truevalue="--UnconnectedCompoundFilter" falsevalue=""
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	155 label="filter non-connected compounds (e.g. salts)" help=""/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	156 <param argument="--IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	157 falsevalue="" label="filter compounds containing non-standard isotopes" help=""/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	158 <param argument="--FilterMinimumElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	159 optional="true" label="Minimum Elements Filter"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	161 2 nitrogens and 3 oxygens">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	162 <expand macro="text-alphanumeric-regex-validator"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	163 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	164 <param argument="--FilterMaximumElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	165 optional="true" label="Maximum Elements Filter"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	167 maximum 5 nitrogens and 7 oxygens">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	168 <expand macro="text-alphanumeric-regex-validator"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	169 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	170 <param argument="--FilterSmartsInclusionList" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	171 optional="true" label="Include substructures"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	173 containing benzene"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	174 <param argument="--FilterSmartsExclusionList" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	175 optional="true" label="Exclude substructures"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	177 containing hydroxyl groups"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	178 <param argument="--FilterIncludedElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	179 optional="true" label="Include elements"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	181 Ex: 'N,O' include compounds containing nitrogen and oxygen" >
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	182 <expand macro="text-alphanumeric-comma-regex-validator"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	183 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	184 <param argument="--FilterIncludedExclusiveElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	185 optional="true" label="Include elements (exclusive)"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	186 help="Filter by presence of defined elements (no other elements are allowed).
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	188 <expand macro="text-alphanumeric-comma-regex-validator"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	189 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	190 <param argument="--FilterExcludedElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	191 optional="true" label="Exclude elements"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	193 compounds including bromine or chlorine">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	194 <expand macro="text-alphanumeric-comma-regex-validator"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	195 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	196 </section>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	197 <section name="PostProcessFilter" title="PostProcessing filters" expanded="False">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	199 max="1" min="0" value="0"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	201 max="100" min="0" value="0"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	202 </section>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	203 </inputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	204 <outputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	205 <data name="results" format="tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	206 </outputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	207 <tests>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	208 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	209 <!-- Test "massbank" style data format -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	210 <param name="input" value="massbank_format.txt"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	211 <param name="schema" value="massbank"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	212 <param name="skip_invalid_adducts" value="false"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	213 <param name="MetFragDatabaseType" value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	214 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	215 <param name="LocalDatabasePath" value="demo_db.csv"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	216 <output name="results" file="metfrag_massbank.tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	217 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	218 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	219 <!-- Test "generic" style data format -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	220 <param name="input" value="generic_format.msp"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	221 <param name="schema" value="msp"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	222 <param name="MetFragDatabaseType" value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	223 <param name="skip_invalid_adducts" value="false"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	224 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	225 <param name="LocalDatabasePath" value="demo_db.csv"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	226 <output name="results" file="metfrag_msp.tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	227 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	228 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	229 <!-- Test PubChem API with "winter" dataset -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	230 <param name="input" value="winter_pos.msp"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	231 <section name="PostProcessFilter">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	232 <param name="score_thrshld" value="0.9"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	233 </section>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	234 <param name="MetFragDatabaseType" value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	235 <output name="results" file="winter_pos.tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	236 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	237 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	238 <!-- Test actual MassBank data for Glucose -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	239 <param name="input" value="RP022611.txt"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	240 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	241 <param name="LocalDatabasePath" value="demo_db.csv"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	242 <output name="results" file="RP022611.tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	243 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	244 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	246 <param name="input" value="RP022611.txt"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	247 <param name="schema" value="massbank"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	248 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	249 <param name="LocalDatabasePath" value="demo_db.csv"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	250 <param name="meta_select_col" value="all"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	251 <output name="results" file="RP022611_all_col.tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	252 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	253 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	255 <param name="input" value="RP022611.txt"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	256 <param name="schema" value="massbank"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	257 <conditional name="suspectlist">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	258 <param name="suspectselector" value="includesuspects"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	259 <conditional name="includesuspects_default_cond">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	260 <param name="includesuspects_default_bool" value="true"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	261 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	262 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	263 <output name="results" file="RP022611_suspect_default.txt"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	264 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	265 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	266 <!-- Test invalid adduct -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	267 <param name="input" value="invalid_adduct.msp"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	268 <param name="skip_invalid_adducts" value="true"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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" computational-metabolomics parents: diff changeset	270 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	271 </tests>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	272 <help>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	273 -------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	274 MetFrag
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	275 -------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	276
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	277 Description
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	278 -----------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	279
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	280 MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	281 a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	282 are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	283 matches gives hints to the quality of the candidate spectrum assignment.
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	284
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	285 Website: http://ipb-halle.github.io/MetFrag/
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	286
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	287 Parameters
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	288 ----------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	289
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	290 \1. MSP file
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	291
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	292 MSP file created using Create MSP tool
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	293
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	294 \2a. MetFragDatabaseType (public databases)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	295
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	296 * PubChem
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	297
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	298 * KEGG
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	299
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	300
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	301 \2b. MetFragDatabaseType (local CSV file database)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	302
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	303
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	304 Custom database file in CSV format with the following structure:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	305
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	306 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	307 \| Identifier \| MonoisotopicMass \| SMILES \| InChI \| Name \|...\|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	308 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	309 \| HMDB0000123 \| 75.03202841 \| NCC(O)=O \| InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) \| Glycine \|...\|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	310 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	311 \| HMDB0002151 \| 78.0139355 \| CS(C)=O \| InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 \| Dimethyl sulfoxide \|...\|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	312 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	313 \| ... \| ... \| ... \| ... \| ... \|...\|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	314 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	315
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	316
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	317 Table continued:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	318
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	319 +---+------------------+-----------------------------+------------------+------------+-------------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	320 \|...\| MolecularFormula \| InChIKey \| InChIKey1 \| InChIKey2 \| InChIKey3 \|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	321 +---+------------------+-----------------------------+------------------+------------+-------------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	322 \|...\| C2H5NO2 \| DHMQDGOQFOQNFH-UHFFFAOYSA-N \| DHMQDGOQFOQNFH \| UHFFFAOYSA \| N \|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	323 +---+------------------+-----------------------------+------------------+------------+-------------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	324 \|...\| C2H6OS \| IAZDPXIOMUYVGZ-UHFFFAOYSA-N \| IAZDPXIOMUYVGZ \| UHFFFAOYSA \| N \|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	325 +---+------------------+-----------------------------+------------------+------------+-------------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	326 \|...\| ... \| ... \| ... \| ... \| ... \|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	327 +---+------------------+-----------------------------+------------------+------------+-------------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	328
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	329
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	330
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	331 \2b. MetFragDatabaseType MetChem
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	332
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	333 MetChem is a modified PubChem database and can be used in replace of PubChem
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	334 for performing API calls to the public PubChem instance.
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	335
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	336 \3. Database Search Relative Mass Deviation - ppm
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	337
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	338 A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses.
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	339
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	340 \4. 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	341
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	342 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	343
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	344 \5. Fragment Peak Match Absolute Mass Deviation (Da)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	345
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	346 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" computational-metabolomics parents: diff changeset	347
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	348 \6. Polarity
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	349
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	350 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: diff changeset	351
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	352 \7. Schema
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	353
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	354 The Schema used by the MSP file (e.g. generic MSP format or MassBank format)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	355
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	356 \8. Suspect list
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	357
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	358 Choose whether to include a file containing a list of suspects.
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	359
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	360 \9. MetFrag Score Types
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	361
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	362 The type of scores MetFrac is using for the calculations. Please do not change the values unless you know what you are doing!
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	363
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	364 \10. MetFrag Score Weights
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	365
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	366 The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100%.
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	367
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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: diff changeset	456 - '[M-H+HCOOH]-': 44.99819,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	457 - '[M+CH3COO]-': 59.01385,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	458 - '[M-H+CH3COOH]-': 59.01385
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	459
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	460 Developers and contributors
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	461 ---------------------------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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 parents: diff changeset	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 parents: diff changeset	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 parents: diff changeset	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 parents: diff changeset	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 parents: diff changeset	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 parents: diff changeset	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 parents: diff changeset	469 </help>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	470 <citations>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	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 parents: diff changeset	472 </citations>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	473 </tool>

Mercurial > repos > computational-metabolomics > metfrag

annotate metfrag.xml @ 0:fd5c0b39569a draft