mspurity_spectralmatching: spectralMatching.xml annotate

annotate spectralMatching.xml @ 0:a8ab07c27338 draft default tip

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"

author	computational-metabolomics
date	Thu, 04 Mar 2021 12:20:23 +0000
parents
children

rev	line source
0 a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	1 <tool id="mspurity_spectralmatching" name="msPurity.spectralMatching" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	2 <description>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	3 Perform spectral matching to MS/MS spectral libraries
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	4 </description>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	5 <macros>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	6 <import>macros.xml</import>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	7 </macros>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	8 <expand macro="requirements"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	10 Rscript '$__tool_directory__/spectralMatching.R'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	11 --outDir=.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	12 --cores=\${GALAXY_SLOTS:-4}
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	13
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	14 #if $Query.q_dbPth_con.q_dbPth_select == 'msPurityData'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	15 --q_defaultDb
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	16 #else if $Query.q_dbPth_con.q_dbPth_select == 'sqlite'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	17 --q_dbPth=$Query.q_dbPth_con.q_dbPth
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	18 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	19
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	20 #if $Library.l_dbPth_con.l_dbPth_select == 'msPurityData'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	21 --l_defaultDb
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	22 #else if $Library.l_dbPth_con.l_dbPth_select == 'sqlite'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	23 --l_dbPth=$Library.l_dbPth_con.l_dbPth
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	24 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	25
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	26 --l_dbType=$Library.l_dbPth_con.l_dbPth_select
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	27 --q_dbType=$Query.q_dbPth_con.q_dbPth_select
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	28
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	29
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	30 --q_ppmPrec=$Query.q_filters.q_ppmPrec
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	31 --l_ppmPrec=$Library.l_filters.l_ppmPrec
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	32
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	33 --q_ppmProd=$Query.q_filters.q_ppmProd
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	34 --l_ppmProd=$Library.l_filters.l_ppmProd
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	35
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	36
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	37 #if $Query.q_filters.q_raThres_cond.q_raThres_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	38 --q_raThres=$Query.q_filters.q_raThres_cond.q_raThres
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	39 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	40
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	41 #if $Library.l_filters.l_raThres_cond.l_raThres_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	42 --l_raThres=$Library.l_filters.l_raThres_cond.l_raThres
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	43 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	44
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	45 #if $Query.q_filters.q_polarity_cond.q_polarity_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	46 --q_polarity=$Query.q_filters.q_polarity_cond.q_polarity
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	47 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	48
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	49 #if $Library.l_filters.l_polarity_cond.l_polarity_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	50 --l_polarity=$Library.l_filters.l_polarity_cond.l_polarity
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	51 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	52
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	53 #if $Query.q_filters.q_purity_cond.q_purity_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	54 --q_purity=$Query.q_filters.q_purity_cond.q_purity
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	55 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	56
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	57 #if $Library.l_filters.l_purity_cond.l_purity_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	58 --l_purity=$Library.l_filters.l_purity_cond.l_purity
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	59 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	60
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	61 #if $Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	62 --q_xcmsGroups=$Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	63 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	64
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	65 #if $Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	66 --l_xcmsGroups=$Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	67 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	68
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	69 #if $Query.q_filters.q_pids_cond.q_pids_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	70 --q_pids=$Query.q_filters.q_pids_cond.q_pids
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	71 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	72
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	73 #if $Library.l_filters.l_pids_cond.l_pids_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	74 --l_pids=$Library.l_filters.l_pids_cond.l_pids
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	75 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	76
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	77 #if $Query.q_filters.q_rtrange_cond.q_rtrange_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	78 --q_rtrangeMin=$Query.q_filters.q_rtrange_cond.q_rtrangeMin
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	79 --q_rtrangeMax=$Query.q_filters.q_rtrange_cond.q_rtrangeMax
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	80 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	81
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	82 #if $Library.l_filters.l_rtrange_cond.l_rtrange_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	83 --l_rtrangeMin=$Library.l_filters.l_rtrange_cond.l_rtrangeMin
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	84 --l_rtrangeMax=$Library.l_filters.l_rtrange_cond.l_rtrangeMax
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	85 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	86
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	87 #if $Query.q_filters.q_accessions_cond.q_accessions_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	88 --q_accessions=$Query.q_filters.q_accessions_cond.q_accessions
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	89 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	90
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	91 #if $Library.l_filters.l_accessions_cond.l_accessions_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	92 --l_accessions=$Library.l_filters.l_accessions_cond.l_accessions
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	93 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	94
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	95
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	96 #if $Query.q_filters.q_sources_cond.q_sources_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	97 --q_sources=$Query.q_filters.q_sources_cond.q_sources
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	98 --q_sourcesUser='$Query.q_filters.q_sources_cond.q_sourcesUser'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	99 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	100
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	101 #if $Library.l_filters.l_sources_cond.l_sources_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	102 --l_sources=$Library.l_filters.l_sources_cond.l_sources
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	103 --l_sourcesUser='$Library.l_filters.l_sources_cond.l_sourcesUser'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	104 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	105
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	106 #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	107 --q_instrumentTypes='$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	108 --q_instrumentTypesUser='$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	109 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	110
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	111 #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	112 --l_instrumentTypes='$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	113 --l_instrumentTypesUser='$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	114 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	115
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	116 #if $Query.q_filters.q_instruments_cond.q_instruments_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	117 --q_instruments=$Query.q_filters.q_instruments_cond.q_instruments
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	118 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	119
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	120 #if $Library.l_filters.l_instruments_cond.l_instruments_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	121 --l_instruments='$Library.l_filters.l_instruments_cond.l_instruments'
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	122 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	123
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	124 #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	125 --q_spectraTypes=$Query.q_filters.q_spectraTypes_cond.q_spectraTypes
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	126 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	127
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	128 #if $Library.l_filters.l_spectraTypes_cond.l_spectraTypes_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	129 --l_spectraTypes=$Library.l_filters.l_spectraTypes_cond.l_spectraTypes
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	130 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	131
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	132 #if $Query.q_filters.q_spectraFilter
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	133 --q_spectraFilter
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	134 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	135
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	136 #if $Library.l_filters.l_spectraFilter
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	137 --l_spectraFilter
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	138 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	139
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	140 #if $General.rttol_cond.rttol_bool
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	141 --rttol=$General.rttol_cond.rttol
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	142 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	143
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	144 --raW=$General.raW
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	145 --mzW=$General.mzW
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	146
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	147 #if $General.updateDb_cond.updateDb
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	148 --updateDb
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	149 #if $General.updateDb_cond.copyDb
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	150 --copyDb
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	151 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	152 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	153
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	154 #if $General.usePrecursors
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	155 --usePrecursors
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	156 #end if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	157
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	158 ]]></command>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	159 <inputs>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	160 <section name="Query" title="Query spectra input and filters" expanded="True">
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	161 <expand macro="sm_input" ql="Query" ql_shrt = "q" user="True" mspuritydatalib="False" msp="False"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	162 help="Query SQLite database - in the standard XCMS msPurity workflow - the output
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	163 of msPurity.createDatabase should be used here. However any SQLite database
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	164 following the schema of as https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	165 <expand macro="filters" ql="Query" ql_shrt="q"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	166 </section>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	167 <section name="Library" title="Library spectra input and filters" expanded="True">
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	168 <expand macro="sm_input" ql="Library" ql_shrt = "l" user="False" mspuritydatalib="True" msp="False"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	169 help="Library SQLite database - in the standard XCMS msPurity workflow - a default
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	170 database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	171 database following the schema of https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	172 <expand macro="filters" ql="Library" ql_shrt="l"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	173 </section>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	174 <section name="General" title="General arguments" expanded="False">
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	175 <conditional name="rttol_cond">
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	176 <param name="rttol_bool" type="boolean" label="Filter on retention time match?"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	177 help="" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	178 <when value="true">
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	179 <param name="rttol" type="float" value="30" min="0"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	180 label="Retention time tolerance (seconds)"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	181 help="Retention time tolerance in seconds to match precursors"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	182 </when>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	183 <when value="false"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	184 </conditional>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	185 <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	186 help="If True, spectra will be filtered by similarity of precursors based on
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	187 the library and query ppm defined tolerance" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	188 <param name="raW" label="Weighting for relative abundance" type="float" value="0.5"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	189 help="Relative abundance weight for spectra (default to 0.5 as determined by
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	190 massbank for ESI data)"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	191 <param name="mzW" label="Weighting for mz" type="float" min="0" value="2"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	192 help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	193 <conditional name="updateDb_cond">
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	194 <param name="updateDb" type="boolean" checked="true"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	195 label="Update database with results?" help="" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	196 <when value="true">
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	197 <param name="copyDb" type="boolean" checked="true"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	198 label="Make a copy of the database?"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	199 help="A copy will be made of the input SQLite target database and the
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	200 results will be added to this copy. When False, the input SQLite
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	201 database will be updated with the matching results. Use False if
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	202 you want to reduce storage space being used."/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	203 </when>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	204 <when value="false"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	205 </conditional>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	206 </section>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	207 </inputs>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	208
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	209 <outputs>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	210 <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	211 from_work_dir="db_with_spectral_matching.sqlite" >
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	212 <filter>create_new_database is True</filter>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	213 </data>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	214 <data name="matches" format="tsv" label="${tool.name} on ${on_string}: matches"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	215 from_work_dir="matched_results.tsv" >
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	216 <filter>spectra_type_q == "scans"</filter>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	217 </data>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	218 <data name="xcms_matches" format="tsv" label="${tool.name} on ${on_string}: XCMS matches"
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	219 from_work_dir="xcms_matched_results.tsv" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	220 </outputs>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	221 <tests>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	222 <test>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	223 <param name="q_dbPth" value="createDatabase_output.sqlite" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	224 <param name="q_spectraTypes_bool" value="true" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	225 <param name="q_spectraTypes" value="inter,av_all" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	226 <param name="l_dbPth_select" value="userdb" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	227 <param name="l_dbPth" value="PR100037.sqlite" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	228 <param name="q_xcmsGroups_bool" value="true" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	229 <param name="l_accessions_bool" value="true" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	230 <param name="q_xcmsGroups" value="14" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	231 <param name="l_accessions" value="PR100037" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	232 <output name="xcms_matches" file="spectralMatching_matched_results.tsv" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	233 <output name="matches" file="spectralMatching_xcms_matched_results.tsv" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	234 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	235 </test>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	236 <test>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	237 <param name="l_instrumentTypes_bool" value="true" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	238 <param name="q_dbPth" value="createDatabase_output.sqlite" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	239 <param name="q_spectraTypes_bool" value="true" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	240 <param name="q_spectraTypes" value="inter,av_all" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	241 <param name="l_dbPth_select" value="userdb" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	242 <param name="l_dbPth" value="PR100037.sqlite" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	243 <param name="q_xcmsGroups_bool" value="true" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	244 <param name="l_accessions_bool" value="true" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	245 <param name="q_xcmsGroups" value="14" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	246 <param name="l_accessions" value="PR100037" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	247 <output name="xcms_matches" file="spectralMatching_matched_results_instrumentTypes.tsv" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	248 <output name="matches" file="spectralMatching_xcms_matched_results_instrumentTypes.tsv" />
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	249 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite" ftype="sqlite" compare="sim_size"/>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	250 </test>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	251 </tests>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	252
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	253 <help><![CDATA[
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	254
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	255 =============================================================
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	256 Spectral matching
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	257 =============================================================
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	258 -----------
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	259 General
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	260 -----------
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	261
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	262
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	263 Perform spectral matching to spectral libraries for an LC-MS/MS dataset.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	264
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	265 The spectral matching is performed from a Query SQLite spectral-database against a Library SQLite spectral-database.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	266
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	267 The SQLite schema of the spectral database here: spectral_database_schema_
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	268
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	269
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	270 The query spectral-database in most cases should contain be the "unknown" spectra database generated the msPurity
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	271 function createDatabase as part of a msPurity-XCMS data processing workflow.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	272
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	273 The library spectral-database in most cases should contain the "known" spectra from either public or user generated resources.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	274 The library SQLite database by default contains data from MoNA including Massbank, HMDB, LipidBlast and GNPS.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	275 A larger_database_ can be download and used from the msp2db github repository.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	276
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	277 To create a user generated library SQLite database the following tool can be used to generate a SQLite database
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	278 from a collection of MSP files: msp2db_.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	279
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	280 It should be noted though, that as long as the schema of the spectral-database is as described here, then any database can be used
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	281 for either the library or query - even allowing for the same database to be used.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	282
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	283 The spectral matching functionality has four main components, spectral filtering, spectral alignment, spectral matching,
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	284 and summarising the results.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	285
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	286 Spectral filtering is simply filtering both the library and query spectra to be search against (e.g. choosing
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	287 the library source, instrument, retention time, precursor PPM tolerance etc).
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	288
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	289 The spectral alignment stage involves aligning the query peaks to the library peaks. The approach used is similar
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	290 to modified pMatch algorithm described in Zhou et al 2015.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	291
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	292 The spectral matching of the aligned spectra is performed against a combined intensity and m/z weighted vector - created for both
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	293 the query and library spectra (wq and wl). See below:
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	294
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	295 .. math::
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	296
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	297 w=intensity^x \cdot mz^y
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	298
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	299
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	300 Where x and y represent weight factors and can be adjusted with the parameters raW and mzW.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	301 Defaults to x=0.5 and y=2 as per MassBank for ESI based mass spectrometry data.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	302
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	303 The aligned weighted vectors are then matched using dot product cosine, reverse dot product cosine and the composite dot product.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	304 See below for dot product cosine equation.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	305
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	306 .. math::
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	307
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	308 dpc = \frac{ w_q \cdot w_l } { \sqrt{Σ{w_{q}{}^2} } \cdot \sqrt{Σ{w_{l}{}^2}}}
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	309
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	310
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	311 Full details of the matching approaches are described in the msPurity_spectral_matching_vignette_
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	312
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	313 --------------------------------------------
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	314 Example LC-MS/MS processing workflow
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	315 --------------------------------------------
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	316
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	317 * Purity assessments
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	318 + (mzML files) -> purityA -> (pa)
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	319 * XCMS processing
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	320 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	321 * Fragmentation processing
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	322 + (xset, pa) -> frag4feature -> filterFragSpectra -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	323
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	324 -----------
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	325 Output
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	326 -----------
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	327
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	328 Database
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	329
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	330 The updated query database (this will have been updated with the annotation results if updateDb argument used)
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	331
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	332
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	333 xcmsMatchedResults
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	334
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	335 If the qeury spectra had XCMS based chromotographic peaks tables (e.g c_peak_groups, c_peaks) in the sqlite database - it will
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	336 be possible to summarise the matches for each XCMS grouped feature. The dataframe contains the following columns
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	337
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	338 * lpid - id in database of library spectra
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	339 * qpid - id in database of query spectra
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	340 * dpc - dot product cosine of the match
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	341 * rdpc - reverse dot product cosine of the match
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	342 * cdpc - composite dot product cosine of the match
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	343 * mcount - number of matching peaks
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	344 * allcount - total number of peaks across both query and library spectra
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	345 * mpercent - percentage of matching peaks across both query and library spectra
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	346 * library_rt - retention time of library spectra
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	347 * query_rt - retention time of query spectra
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	348 * rtdiff - difference between library and query retention time
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	349 * library_precursor_mz - library precursor mz
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	350 * query_precursor_mz - query precursor mz
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	351 * library_precursor_ion_purity - library precursor ion purity
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	352 * query_precursor_ion_purity - query precursor ion purity
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	353 * library_accession - library accession value (unique string or number given to eith MoNA or Massbank data entires)
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	354 * library_precursor_type - library precursor type (i.e. adduct)
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	355 * library_entry_name - Name given to the library spectra
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	356 * inchikey - inchikey of the matched library spectra
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	357 * library_source_name - source of the spectra (e.g. massbank, gnps)
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	358 * library_compound_name - name of compound spectra was obtained from
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	359
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	360 matchedResults
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	361
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	362 All matched results from the query spectra to the library spectra. Contains the same as above
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	363 without the XCMS details. This table is useful to observe spectral matching results
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	364 for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features.
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	365
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	366
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	367 .. _spectral_database_schema: https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	368 .. _larger_database: https://github.com/computational-metabolomics/msp2db/releases
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	369 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	370 .. _msPurity_spectral_matching_vignette: https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	371
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	372 ]]></help>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	373
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	374 <expand macro="citations"> </expand>
a8ab07c27338 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb" computational-metabolomics parents: diff changeset	375 </tool>

Mercurial > repos > computational-metabolomics > mspurity_spectralmatching

annotate spectralMatching.xml @ 0:a8ab07c27338 draft default tip