metfrag: metfrag.xml annotate

annotate metfrag.xml @ 2:f151ee133612 draft default tip

"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

author	computational-metabolomics
date	Tue, 14 Jul 2020 07:41:53 -0400
parents	9ee2e2ceb2c9
children

rev	line source
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	1 <tool id="metfrag" name="MetFrag" version="2.4.5+galaxy3" profile="18.01">
0 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
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	54 $output_cl
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	55
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	56 $PreProcessFilter.UnconnectedCompoundFilter
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	57 $PreProcessFilter.IsotopeFilter
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	58
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	59 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	60 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	61 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	62 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	63 --FilterIncludedElements '$PreProcessFilter.FilterIncludedElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	64 --FilterExcludedElements '$PreProcessFilter.FilterExcludedElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	65 --FilterIncludedExclusiveElements '$PreProcessFilter.FilterIncludedExclusiveElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	66
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	67 #if $adducts_cond.adducts_selector == 'select':
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	68 #for $a in $adducts_cond.adducts
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	69 --adducts $a
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	70 #end for
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	71 #elif $adducts_cond.adducts_selector == 'all':
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	72 #if $polarity == 'pos':
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	73 --adducts [M+H]+
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	74 --adducts [M+NH4]+
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	75 --adducts [M+Na]+
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	76 --adducts [M+K]+
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	77 --adducts [M+CH3OH+H]+
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	78 --adducts [M+ACN+H]+
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	79 --adducts [M+ACN+Na]+
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	80 --adducts [M+2ACN+H]+
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	81 #elif $polarity == 'neg':
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	82 --adducts [M-H]-
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	83 --adducts [M+Cl]-
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	84 --adducts [M+HCOO]-
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	85 --adducts [M+CH3COO]-
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	86 #end if
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	87 #end if
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	88
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	89 $skip_invalid_adducts
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	90 --score_thrshld $PostProcessFilter.score_thrshld
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	91 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	92
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	93 ]]></command>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	94 <inputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	95 <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	96 <conditional name="db_select">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	97 <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	98 <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	99 <option value="KEGG">KEGG</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	100 <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	101 <option value="MetChem">MetChem</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	102 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	103 <when value="MetChem">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	104 <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	105 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	106 <when value="LocalCSV">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	107 <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	108 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	109 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	110 <when value="KEGG"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	111 <when value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	112 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	113 <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	114 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	115 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	116 vs. the measured masses"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	117 <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	118 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	119 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	120 <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	121 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	122 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	123 <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	124 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	125 <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	126 <option value="neg">Negative</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	127 </param>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	128
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	129 <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	130 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	131 <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	132 <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	133 <option value="massbank">MassBank</option>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	134 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	135 <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	136 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	137 help="The MetFrag output can have additional meta data columns added, these can be either extracted
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	138 from the MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	139 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	140 e.g. 'MZ:100.2 \| RT:20 \| xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns">
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	141 <option value="name" >Extra metadata columns from the Name or RECORD_TITLE</option>
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	142 <option value="name_split">Extra metadata columns from the Name or RECORD_TITLE (each column is split on "\|" and ":" ) </option>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	143 <option value="all" selected="true">Extra metadata columns from MSP parameters</option>
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	144 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	145 <conditional name="suspectlist">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	146 <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	147 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	148 <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	149 <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	150 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	151 <when value="includesuspects">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	152 <conditional name="includesuspects_default_cond">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	153 <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	154 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	155 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	156 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	157 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	158 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	159 <when value="true"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	160 <when value="false">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	161 <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	162 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	163 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	164 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	165 <expand macro="metfrag_scoring"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	166 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	167 <when value="excludesuspects">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	168 <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	169 </when>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	170 </conditional>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	171
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	172 <conditional name="adducts_cond">
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	173 <param name="adducts_selector" type="select" label="How to handle adducts"
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	174 help="Choose whether to include a suspect list">
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	175 <option value="msp" selected="True">Use adducts defined in MSP file</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	176 <option value="select" >Select from list</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	177 <option value="all" >Use all available adducts for either pos or neg ionisation mode</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	178 </param>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	179 <when value="msp">
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	180 </when>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	181 <when value="select">
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	182 <param argument="--adducts" label="Select adducts" type="select" help="" multiple="true" display="checkboxes">
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	183 <option value="[M+H]+" selected="True">[M+H]+ 1.007276</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	184 <option value="[M+NH4]+">[M+NH4]+ 18.034374</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	185 <option value="[M+Na]+">[M+Na]+ 22.989218</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	186 <option value="[M+K]+">[M+K]+ 38.963158</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	187 <option value="[M+CH3OH+H]+">[M+CH3OH+H]+ 33.033489</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	188 <option value="[M+ACN+H]+">[M+ACN+H]+ 42.033823</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	189 <option value="[M+ACN+Na]+">[M+ACN+Na]+ 64.015765</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	190 <option value="[M+2ACN+H]+">[M+2ACN+H]+ 83.06037</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	191 <option value="[M-H]-" >[M-H]- -1.007276</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	192 <option value="[M+Cl]-">[M+Cl]- 34.969402</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	193 <option value="[M+HCOO]-">[M+HCOO]- 44.99819</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	194 <option value="[M+CH3COO]-">[M+CH3COO]- 59.01385</option>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	195 </param>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	196 </when>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	197 <when value="all">
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	198 </when>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	199 </conditional>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	200
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	201 <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	202 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	203 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	204 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	205 of [M+H]+ for pos data or [M-H]- for neg data should be used"/>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	206
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	207 <param argument="minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	208 <param argument="--output_cl" type="boolean" checked="true"
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	209 truevalue="--output_cl" falsevalue=""
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	210 label="Output the MetFrag command line call" help="This will output all the parameters used
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	211 for each MetFrag command line call (including the fragment peaks)"/>
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	212 <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	213 <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	214 truevalue="--UnconnectedCompoundFilter" falsevalue=""
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	215 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	216 <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	217 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	218 <param argument="--FilterMinimumElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	219 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	220 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	221 2 nitrogens and 3 oxygens">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	222 <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	223 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	224 <param argument="--FilterMaximumElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	225 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	226 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	227 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	228 <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	229 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	230 <param argument="--FilterSmartsInclusionList" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	231 optional="true" label="Include substructures"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	232 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	233 containing benzene"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	234 <param argument="--FilterSmartsExclusionList" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	235 optional="true" label="Exclude substructures"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	236 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	237 containing hydroxyl groups"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	238 <param argument="--FilterIncludedElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	239 optional="true" label="Include elements"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	240 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	241 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	242 <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	243 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	244 <param argument="--FilterIncludedExclusiveElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	245 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	246 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	247 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	248 <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	249 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	250 <param argument="--FilterExcludedElements" type="text"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	251 optional="true" label="Exclude elements"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	252 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	253 compounds including bromine or chlorine">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	254 <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	255 </param>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	256 </section>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	257 <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	258 <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	259 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	260 <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	261 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	262 </section>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	263 </inputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	264 <outputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	265 <data name="results" format="tabular"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	266 </outputs>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	267 <tests>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	268 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	269 <!-- Test "massbank" style data format -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	270 <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	271 <param name="schema" value="massbank"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	272 <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	273 <param name="MetFragDatabaseType" value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	274 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	275 <param name="LocalDatabasePath" value="demo_db.csv"/>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	276 <param name="meta_select_col" value="name"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	277 <param name="output_cl" value="false"/>
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	278 <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	279 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	280 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	281 <!-- Test "generic" style data format -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	282 <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	283 <param name="schema" value="msp"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	284 <param name="MetFragDatabaseType" value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	285 <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	286 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	287 <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	288 <output name="results" file="metfrag_msp.tabular"/>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	289 <param name="meta_select_col" value="name"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	290 <param name="output_cl" value="false"/>
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	291 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	292 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	293 <!-- 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	294 <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	295 <section name="PostProcessFilter">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	296 <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	297 </section>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	298 <param name="MetFragDatabaseType" value="PubChem"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	299 <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	300 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	301 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	302 <!-- 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	303 <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	304 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	305 <param name="LocalDatabasePath" value="demo_db.csv"/>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	306 <param name="meta_select_col" value="name"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	307 <param name="output_cl" value="false"/>
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	308 <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	309 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	310 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	311 <!-- 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	312 <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	313 <param name="schema" value="massbank"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	314 <param name="MetFragDatabaseType" value="LocalCSV"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	315 <param name="LocalDatabasePath" value="demo_db.csv"/>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	316 <param name="output_cl" value="false"/>
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	317 <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	318 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	319 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	320 <!-- 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	321 <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	322 <param name="schema" value="massbank"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	323 <conditional name="suspectlist">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	324 <param name="suspectselector" value="includesuspects"/>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	325 <conditional name="includesuspects_default_cond">
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	326 <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	327 </conditional>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	328 </conditional>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	329 <param name="meta_select_col" value="name"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	330 <param name="output_cl" value="false"/>
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	331 <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	332 </test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	333 <test>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	334 <!-- Test invalid adduct -->
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	335 <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	336 <param name="skip_invalid_adducts" value="true"/>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	337 <param name="meta_select_col" value="name"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	338 <param name="output_cl" value="false"/>
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	339 <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	340 </test>
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	341 <test>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	342 <!-- Test all adducts-->
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	343 <param name="input" value="RP022611.txt"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	344 <param name="schema" value="massbank"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	345 <param name="polarity" value="neg"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	346 <param name="skip_invalid_adducts" value="false"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	347 <param name="MetFragDatabaseType" value="PubChem"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	348 <param name="MetFragDatabaseType" value="LocalCSV"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	349 <param name="LocalDatabasePath" value="demo_db.csv"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	350 <param name="meta_select_col" value="name"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	351 <param name="output_cl" value="false"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	352 <output name="results" file="RP022611_all_adducts.tabular"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	353 <conditional name="adducts_cond">
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	354 <param name="adducts_selector" value="all"/>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	355 </conditional>
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	356 </test>
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	357 </tests>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	358 <help>
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 MetFrag
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
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	363 Description
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	364 -----------
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 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	367 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	368 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	369 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	370
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	371 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	372
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	373 Parameters
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	374 ----------
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 \1. MSP file
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 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	379
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	380 \2a. MetFragDatabaseType (public databases)
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 * PubChem
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	383
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	384 * KEGG
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	385
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 \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	388
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 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	391
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 \| Identifier \| MonoisotopicMass \| SMILES \| InChI \| Name \|...\|
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 \| 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	396 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	397 \| 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	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 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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 Table continued:
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 +---+------------------+-----------------------------+------------------+------------+-------------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	406 \|...\| MolecularFormula \| InChIKey \| InChIKey1 \| InChIKey2 \| InChIKey3 \|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	407 +---+------------------+-----------------------------+------------------+------------+-------------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	408 \|...\| 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	409 +---+------------------+-----------------------------+------------------+------------+-------------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	410 \|...\| 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	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 +---+------------------+-----------------------------+------------------+------------+-------------+
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
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	417 \2b. MetFragDatabaseType MetChem
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	418
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	419 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	420 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	421
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	422 \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	423
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	424 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	425
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	426 \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	427
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	428 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	429
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	430 \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	431
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	432 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	433
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	434 \6. Polarity
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 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	437
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	438 \7. Schema
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	439
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	440 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	441
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	442 \8. Suspect list
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	443
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	444 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	445
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	446 \9. MetFrag Score Types
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	447
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	448 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	449
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	450 \10. MetFrag Score Weights
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	451
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	452 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	453
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	454 \11. MetFrag Database Type
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	455
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	456 Database to choose from.
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	457
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	458 \12. minMSMSpeaks
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 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	461
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	462 \13. PreProcessFilter
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	463
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	464 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	465
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	466 \14. PostProcessFilter
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	467
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	468 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	469 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	470
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	471 Output
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	472 -------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	473
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	474 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	475
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	476 +-------------+--------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	477 \| adduct \| name \|...\|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	478 +-------------+--------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	479 \| [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	480 +-------------+--------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	481 \| [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	482 +-------------+--------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	483 \| ... \| ... \|...\|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	484 +-------------+--------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	485
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	486 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	487
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	488 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	489 \|...\| sample_name \| ExplPeaks \| FormulasOfExplPeaks \| ... \|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	490 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	491 \|...\| 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	492 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	493 \|...\| 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	494 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	495 \|...\| ... \| ... \| ... \| ... \|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	496 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	497
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	498
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	499 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	500
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	501 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	502 \|...\| 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	503 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	504 \|...\| 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	505 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	506 \|...\| 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	507 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	508 \|...\| ... \| ... \| ... \| ... \| ... \|...\|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	509 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	510
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	511 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	512
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	513
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	514 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	515 \|...\| 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	516 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	517 \|...\| 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	518 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	519 \|...\| 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	520 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	521 \|...\| ... \| ... \| ... \| ... \| ... \| ... \| ... \|
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	522 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	523
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	524
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	525 Additional notes
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	526 --------------------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	527
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	528 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	529 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	530
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	531 - '[M+H]+': 1.007276,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	532 - '[M+NH4]+': 18.034374,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	533 - '[M+Na]+': 22.989218,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	534 - '[M+K]+': 38.963158,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	535 - '[M+CH3OH+H]+': 33.033489,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	536 - '[M+ACN+H]+': 42.033823,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	537 - '[M+ACN+Na]+': 64.015765,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	538 - '[M+2ACN+H]+': 83.06037,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	539 - '[M-H]-': -1.007276,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	540 - '[M+Cl]-': 34.969402,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	541 - '[M+HCOO]-': 44.99819,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	542 - '[M-H+HCOOH]-': 44.99819,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	543 - '[M+CH3COO]-': 59.01385,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	544 - '[M-H+CH3COOH]-': 59.01385
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	545
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	546 Developers and contributors
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	547 ---------------------------
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	548 - 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	549 - 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	550 - 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	551 - 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	552 - 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	553 - 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	554 - 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	555 </help>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	556 <citations>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	557 <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	558 </citations>
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	559 </tool>

Mercurial > repos > computational-metabolomics > metfrag

annotate metfrag.xml @ 2:f151ee133612 draft default tip