Mercurial > repos > tomnl > mspurity_spectralmatching

annotate spectralMatching.xml @ 15:945e73261fbb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:30:07 +0000
parents 499c26566a7a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
103d2613b3a7 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3
tomnl
parents: 10
diff changeset
1 <tool id="mspurity_spectralmatching" name="msPurity.spectralMatching" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
2 <description>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
3 Perform spectral matching to MS/MS spectral libraries
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
4 </description>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
5 <macros>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
6 <import>macros.xml</import>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
7 </macros>
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
8 <expand macro="requirements"/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
10 Rscript '$__tool_directory__/spectralMatching.R'
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
11 --outDir=.
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
12 --cores=\${GALAXY_SLOTS:-4}
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
13
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
14 #if $Query.q_dbPth_con.q_dbPth_select == 'msPurityData'
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
15 --q_defaultDb
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
16 #else if $Query.q_dbPth_con.q_dbPth_select == 'sqlite'
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
17 --q_dbPth=$Query.q_dbPth_con.q_dbPth
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
18 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
19
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
20 #if $Library.l_dbPth_con.l_dbPth_select == 'msPurityData'
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
21 --l_defaultDb
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
22 #else if $Library.l_dbPth_con.l_dbPth_select == 'userdb_sqlite'
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
23 --l_dbPth=$Library.l_dbPth_con.l_dbPth
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
24 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
25
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
26 --l_dbType=$Library.l_dbPth_con.l_dbPth_select
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
27 --q_dbType=$Query.q_dbPth_con.q_dbPth_select
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
28
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
29
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
30 --q_ppmPrec=$Query.q_filters.q_ppmPrec
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
31 --l_ppmPrec=$Library.l_filters.l_ppmPrec
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
32
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
33 --q_ppmProd=$Query.q_filters.q_ppmProd
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
34 --l_ppmProd=$Library.l_filters.l_ppmProd
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
35
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
36
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
37 #if $Query.q_filters.q_raThres_cond.q_raThres_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
38 --q_raThres=$Query.q_filters.q_raThres_cond.q_raThres
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
39 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
40
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
41 #if $Library.l_filters.l_raThres_cond.l_raThres_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
42 --l_raThres=$Library.l_filters.l_raThres_cond.l_raThres
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
43 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
44
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
45 #if $Query.q_filters.q_polarity_cond.q_polarity_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
46 --q_polarity=$Query.q_filters.q_polarity_cond.q_polarity
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
47 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
48
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
49 #if $Library.l_filters.l_polarity_cond.l_polarity_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
50 --l_polarity=$Library.l_filters.l_polarity_cond.l_polarity
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
51 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
52
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
53 #if $Query.q_filters.q_purity_cond.q_purity_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
54 --q_purity=$Query.q_filters.q_purity_cond.q_purity
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
55 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
56
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
57 #if $Library.l_filters.l_purity_cond.l_purity_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
58 --l_purity=$Library.l_filters.l_purity_cond.l_purity
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
59 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
60
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
61 #if $Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
62 --q_xcmsGroups=$Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
63 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
64
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
65 #if $Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
66 --l_xcmsGroups=$Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
67 #end if
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
68
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
69 #if $Query.q_filters.q_pids_cond.q_pids_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
70 --q_pids=$Query.q_filters.q_pids_cond.q_pids
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
71 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
72
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
73 #if $Library.l_filters.l_pids_cond.l_pids_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
74 --l_pids=$Library.l_filters.l_pids_cond.l_pids
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
75 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
76
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
77 #if $Query.q_filters.q_rtrange_cond.q_rtrange_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
78 --q_rtrangeMin=$Query.q_filters.q_rtrange_cond.q_rtrangeMin
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
79 --q_rtrangeMax=$Query.q_filters.q_rtrange_cond.q_rtrangeMax
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
80 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
81
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
82 #if $Library.l_filters.l_rtrange_cond.l_rtrange_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
83 --l_rtrangeMin=$Library.l_filters.l_rtrange_cond.l_rtrangeMin
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
84 --l_rtrangeMax=$Library.l_filters.l_rtrange_cond.l_rtrangeMax
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
85 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
86
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
87 #if $Query.q_filters.q_accessions_cond.q_accessions_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
88 --q_accessions=$Query.q_filters.q_accessions_cond.q_accessions
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
89 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
90
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
91 #if $Library.l_filters.l_accessions_cond.l_accessions_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
92 --l_accessions=$Library.l_filters.l_accessions_cond.l_accessions
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
93 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
94
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
95
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
96 #if $Query.q_filters.q_sources_cond.q_sources_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
97 --q_sources=$Query.q_filters.q_sources_cond.q_sources
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
98 --q_sourcesUser='$Query.q_filters.q_sources_cond.q_sourcesUser'
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
99 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
100
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
101 #if $Library.l_filters.l_sources_cond.l_sources_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
102 --l_sources=$Library.l_filters.l_sources_cond.l_sources
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
103 --l_sourcesUser='$Library.l_filters.l_sources_cond.l_sourcesUser'
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
104 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
105
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
106 #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
107 --q_instrumentTypes='$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes'
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
108 --q_instrumentTypesUser='$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser'
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
109 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
110
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
111 #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
112 --l_instrumentTypes='$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes'
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
113 --l_instrumentTypesUser='$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser'
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
114 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
115
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
116 #if $Query.q_filters.q_instruments_cond.q_instruments_bool
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
117 --q_instruments=$Query.q_filters.q_instruments_cond.q_instruments
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
118 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
119
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
120 #if $Library.l_filters.l_instruments_cond.l_instruments_bool
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
121 --l_instruments='$Library.l_filters.l_instruments_cond.l_instruments'
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
122 #end if
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
123
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
124 #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
125 --q_spectraTypes=$Query.q_filters.q_spectraTypes_cond.q_spectraTypes
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
126 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
127
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
128 #if $Library.l_filters.l_spectraTypes_cond.l_spectraTypes_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
129 --l_spectraTypes=$Library.l_filters.l_spectraTypes_cond.l_spectraTypes
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
130 #end if
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
131
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
132 #if $Query.q_filters.q_spectraFilter
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
133 --q_spectraFilter
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
134 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
135
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
136 #if $Library.l_filters.l_spectraFilter
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
137 --l_spectraFilter
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
138 #end if
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
139
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
140 #if $General.rttol_cond.rttol_bool
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
141 --rttol=$General.rttol_cond.rttol
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
142 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
143
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
144 --raW=$General.raW
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
145 --mzW=$General.mzW
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
146
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
147 #if $General.updateDb_cond.updateDb
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
148 --updateDb
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
149 #if $General.updateDb_cond.copyDb
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
150 --copyDb
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
151 #end if
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
152 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
153
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
154 #if $General.usePrecursors
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
155 --usePrecursors
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
156 #end if
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
157
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
158 ]]></command>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
159 <inputs>
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
160 <section name="Query" title="Query spectra input and filters" expanded="True">
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
161 <expand macro="sm_input" ql="Query" ql_shrt = "q" user="True" mspuritydatalib="False" msp="False"
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
162 help="Query SQLite database - in the standard XCMS msPurity workflow - the output
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
163 of msPurity.createDatabase should be used here. However any SQLite database
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
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"/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
165 <expand macro="filters" ql="Query" ql_shrt="q"/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
166 </section>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
167 <section name="Library" title="Library spectra input and filters" expanded="True">
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
168 <expand macro="sm_input" ql="Library" ql_shrt = "l" user="False" mspuritydatalib="True" msp="False"
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
169 help="Library SQLite database - in the standard XCMS msPurity workflow - a default
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
170 database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
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"/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
172 <expand macro="filters" ql="Library" ql_shrt="l"/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
173 </section>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
174 <section name="General" title="General arguments" expanded="False">
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
175 <conditional name="rttol_cond">
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
176 <param name="rttol_bool" type="boolean" label="Filter on retention time match?"
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
177 help="" />
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
178 <when value="true">
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
179 <param name="rttol" type="float" value="30" min="0"
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
180 label="Retention time tolerance (seconds)"
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
181 help="Retention time tolerance in seconds to match precursors"/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
182 </when>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
183 <when value="false"/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
184 </conditional>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
185 <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?"
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
186 help="If True, spectra will be filtered by similarity of precursors based on
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
187 the library and query ppm defined tolerance" />
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
188 <param name="raW" label="Weighting for relative abundance" type="float" value="0.5"
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
189 help="Relative abundance weight for spectra (default to 0.5 as determined by
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
190 massbank for ESI data)"/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
191 <param name="mzW" label="Weighting for mz" type="float" min="0" value="2"
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
192 help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
193 <conditional name="updateDb_cond">
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
194 <param name="updateDb" type="boolean" checked="true"
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
195 label="Update database with results?" help="" />
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
196 <when value="true">
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
197 <param name="copyDb" type="boolean" checked="true"
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
198 label="Make a copy of the database?"
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
199 help="A copy will be made of the input SQLite target database and the
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
200 results will be added to this copy. When False, the input SQLite
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
201 database will be updated with the matching results. Use False if
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
202 you want to reduce storage space being used."/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
203 </when>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
204 <when value="false"/>
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
205 </conditional>
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
206 </section>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
207 </inputs>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
208
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
209 <outputs>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
210 <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results"
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
211 from_work_dir="db_with_spectral_matching.sqlite" >
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
212 <filter>create_new_database is True</filter>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
213 </data>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
214 <data name="matches" format="tsv" label="${tool.name} on ${on_string}: matches"
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
215 from_work_dir="matched_results.tsv" >
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
216 <filter>spectra_type_q == "scans"</filter>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
217 </data>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
218 <data name="xcms_matches" format="tsv" label="${tool.name} on ${on_string}: XCMS matches"
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
219 from_work_dir="xcms_matched_results.tsv" />
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
220 </outputs>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
221 <tests>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
222 <test>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
223 <param name="q_dbPth" value="createDatabase_output.sqlite" />
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
224 <param name="l_dbPth_select" value="userdb" />
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
225 <param name="l_dbPth" value="PR100037.sqlite" />
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
226 <param name="q_xcmsGroups_bool" value="true" />
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
227 <param name="l_accessions_bool" value="true" />
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
228 <param name="q_xcmsGroups" value="14" />
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
229 <param name="l_accessions" value="PR100037" />
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
230 <output name="xcms_matches" file="spectralMatching_matched_results.tsv" />
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
231 <output name="matches" file="spectralMatching_xcms_matched_results.tsv" />
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
232 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
233 </test>
14
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
234 <test>
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
235 <param name="l_instrumentTypes_bool" value="true" />
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
236 <param name="q_dbPth" value="createDatabase_output.sqlite" />
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
237 <param name="l_dbPth_select" value="userdb" />
14
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
238 <param name="l_dbPth" value="PR100037.sqlite" />
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
239 <param name="q_xcmsGroups_bool" value="true" />
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
240 <param name="l_accessions_bool" value="true" />
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
241 <param name="q_xcmsGroups" value="14" />
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
242 <param name="l_accessions" value="PR100037" />
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
243 <output name="xcms_matches" file="spectralMatching_matched_results_instrumentTypes.tsv" />
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
244 <output name="matches" file="spectralMatching_xcms_matched_results_instrumentTypes.tsv" />
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
245 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite" ftype="sqlite" compare="sim_size"/>
499c26566a7a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit ee6b57a84748b56c26646f7c37feabcb87a25430
tomnl
parents: 13
diff changeset
246 </test>
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
247 </tests>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
248
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
249 <help><![CDATA[
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
250
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
251 =============================================================
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
252 Spectral matching
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
253 =============================================================
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
254 -----------
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
255 General
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
256 -----------
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
257
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
258
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
259 Perform spectral matching to spectral libraries for an LC-MS/MS dataset.
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
260
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
261 The spectral matching is performed from a **Query** SQLite spectral-database against a **Library** SQLite spectral-database.
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
262
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
263 The SQLite schema of the spectral database here: spectral_database_schema_
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
264
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
265
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
266 The query spectral-database in most cases should contain be the "unknown" spectra database generated the msPurity
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
267 function createDatabase as part of a msPurity-XCMS data processing workflow.
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
268
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
269 The library spectral-database in most cases should contain the "known" spectra from either public or user generated resources.
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
270 The library SQLite database by default contains data from MoNA including Massbank, HMDB, LipidBlast and GNPS.
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
271 A larger_database_ can be download and used from the msp2db github repository.
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
272
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
273 To create a user generated library SQLite database the following tool can be used to generate a SQLite database
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
274 from a collection of MSP files: msp2db_.
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
275
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
276 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
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
277 for either the library or query - even allowing for the same database to be used.
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
278
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
279 The spectral matching functionality has four main components, spectral filtering, spectral alignment, spectral matching,
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
280 and summarising the results.
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
281
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
282 Spectral filtering is simply filtering both the library and query spectra to be search against (e.g. choosing
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
283 the library source, instrument, retention time, precursor PPM tolerance etc).
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
284
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
285 The spectral alignment stage involves aligning the query peaks to the library peaks. The approach used is similar
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
286 to modified pMatch algorithm described in Zhou et al 2015.
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
287
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
288 The spectral matching of the aligned spectra is performed against a combined intensity and m/z weighted vector - created for both
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
289 the query and library spectra (wq and wl). See below:
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
290
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
291 .. math::
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
292
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
293 w=intensity^x \cdot mz^y
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
294
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
295
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
296 Where x and y represent weight factors and can be adjusted with the parameters raW and mzW.
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
297 Defaults to x=0.5 and y=2 as per MassBank for ESI based mass spectrometry data.
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
298
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
299 The aligned weighted vectors are then matched using dot product cosine, reverse dot product cosine and the composite dot product.
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
300 See below for dot product cosine equation.
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
301
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
302 .. math::
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
303
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
304 dpc = \frac{ w_q \cdot w_l } { \sqrt{Σ{w_{q}{}^2} } \cdot \sqrt{Σ{w_{l}{}^2}}}
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
305
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
306
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
307 Full details of the matching approaches are described in the msPurity_spectral_matching_vignette_
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
308
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
309 --------------------------------------------
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
310 Example LC-MS/MS processing workflow
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
311 --------------------------------------------
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
312
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
313 * Purity assessments
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
314 + (mzML files) -> purityA -> (pa)
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
315 * XCMS processing
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
316 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
317 * Fragmentation processing
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
318 + (xset, pa) -> frag4feature -> filterFragSpectra -> averageAllFragSpectra -> createDatabase -> **spectralMatching** -> (sqlite spectral database)
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
319
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
320 -----------
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
321 Output
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
322 -----------
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
323
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
324 **Database**
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
325
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
326 The updated query database (this will have been updated with the annotation results if updateDb argument used)
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
327
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
328
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
329 **xcmsMatchedResults**
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
330
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
331 If the qeury spectra had XCMS based chromotographic peaks tables (e.g c_peak_groups, c_peaks) in the sqlite database - it will
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
332 be possible to summarise the matches for each XCMS grouped feature. The dataframe contains the following columns
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
333
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
334 * lpid - id in database of library spectra
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
335 * qpid - id in database of query spectra
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
336 * dpc - dot product cosine of the match
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
337 * rdpc - reverse dot product cosine of the match
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
338 * cdpc - composite dot product cosine of the match
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
339 * mcount - number of matching peaks
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
340 * allcount - total number of peaks across both query and library spectra
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
341 * mpercent - percentage of matching peaks across both query and library spectra
12
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
342 * library_rt - retention time of library spectra
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
343 * query_rt - retention time of query spectra
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
344 * rtdiff - difference between library and query retention time
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
345 * library_precursor_mz - library precursor mz
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
346 * query_precursor_mz - query precursor mz
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
347 * library_precursor_ion_purity - library precursor ion purity
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
348 * query_precursor_ion_purity - query precursor ion purity
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
349 * library_accession - library accession value (unique string or number given to eith MoNA or Massbank data entires)
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
350 * library_precursor_type - library precursor type (i.e. adduct)
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
351 * library_entry_name - Name given to the library spectra
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
352 * inchikey - inchikey of the matched library spectra
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
353 * library_source_name - source of the spectra (e.g. massbank, gnps)
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
354 * library_compound_name - name of compound spectra was obtained from
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
355
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
356 **matchedResults**
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
357
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
358 All matched results from the query spectra to the library spectra. Contains the same as above
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
359 without the XCMS details. This table is useful to observe spectral matching results
e131f2fb0f97 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 11
diff changeset
360 for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features.
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
361
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
362
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
363 .. _spectral_database_schema: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
364 .. _larger_database: https://github.com/computational-metabolomics/msp2db/releases
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
365 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
366 .. _msPurity_spectral_matching_vignette: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
367
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
368 ]]></help>
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
369
15
945e73261fbb planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 14
diff changeset
370 <expand macro="citations"> </expand>
0
21a19280e7ae planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
371 </tool>