Mercurial > repos > computational-metabolomics > mspurity_spectralmatching

annotate spectralMatching.xml @ 4:aee10d29e82c draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
author computational-metabolomics
date Mon, 10 Aug 2020 08:39:40 -0400
parents 5ff9d40c7a42
children fecfe8c80e25
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5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 <tool id="mspurity_spectralmatching" name="msPurity.spectralMatching" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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2 <description>
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3 Perform spectral matching to MS/MS spectral libraries
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript '$__tool_directory__/spectralMatching.R'
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11 --outDir=.
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12 --cores=\${GALAXY_SLOTS:-4}
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14 #if $Query.q_dbPth_con.q_dbPth_select == 'msPurityData'
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15 --q_defaultDb
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16 #else if $Query.q_dbPth_con.q_dbPth_select == 'sqlite'
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17 --q_dbPth=$Query.q_dbPth_con.q_dbPth
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18 #end if
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20 #if $Library.l_dbPth_con.l_dbPth_select == 'msPurityData'
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21 --l_defaultDb
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22 #else if $Library.l_dbPth_con.l_dbPth_select == 'sqlite'
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23 --l_dbPth=$Library.l_dbPth_con.l_dbPth
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24 #end if
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26 --l_dbType=$Library.l_dbPth_con.l_dbPth_select
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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27 --q_dbType=$Query.q_dbPth_con.q_dbPth_select
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28
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29
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30 --q_ppmPrec=$Query.q_filters.q_ppmPrec
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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31 --l_ppmPrec=$Library.l_filters.l_ppmPrec
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32
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33 --q_ppmProd=$Query.q_filters.q_ppmProd
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34 --l_ppmProd=$Library.l_filters.l_ppmProd
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37 #if $Query.q_filters.q_raThres_cond.q_raThres_bool
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38 --q_raThres=$Query.q_filters.q_raThres_cond.q_raThres
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39 #end if
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40
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41 #if $Library.l_filters.l_raThres_cond.l_raThres_bool
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42 --l_raThres=$Library.l_filters.l_raThres_cond.l_raThres
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43 #end if
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44
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45 #if $Query.q_filters.q_polarity_cond.q_polarity_bool
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46 --q_polarity=$Query.q_filters.q_polarity_cond.q_polarity
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47 #end if
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48
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49 #if $Library.l_filters.l_polarity_cond.l_polarity_bool
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50 --l_polarity=$Library.l_filters.l_polarity_cond.l_polarity
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51 #end if
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52
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53 #if $Query.q_filters.q_purity_cond.q_purity_bool
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54 --q_purity=$Query.q_filters.q_purity_cond.q_purity
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55 #end if
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56
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57 #if $Library.l_filters.l_purity_cond.l_purity_bool
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58 --l_purity=$Library.l_filters.l_purity_cond.l_purity
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59 #end if
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61 #if $Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups_bool
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62 --q_xcmsGroups=$Query.q_filters.q_xcmsGroups_cond.q_xcmsGroups
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63 #end if
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64
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65 #if $Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups_bool
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66 --l_xcmsGroups=$Library.l_filters.l_xcmsGroups_cond.l_xcmsGroups
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67 #end if
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68
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69 #if $Query.q_filters.q_pids_cond.q_pids_bool
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70 --q_pids=$Query.q_filters.q_pids_cond.q_pids
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71 #end if
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72
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73 #if $Library.l_filters.l_pids_cond.l_pids_bool
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74 --l_pids=$Library.l_filters.l_pids_cond.l_pids
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75 #end if
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77 #if $Query.q_filters.q_rtrange_cond.q_rtrange_bool
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78 --q_rtrangeMin=$Query.q_filters.q_rtrange_cond.q_rtrangeMin
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79 --q_rtrangeMax=$Query.q_filters.q_rtrange_cond.q_rtrangeMax
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80 #end if
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81
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82 #if $Library.l_filters.l_rtrange_cond.l_rtrange_bool
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83 --l_rtrangeMin=$Library.l_filters.l_rtrange_cond.l_rtrangeMin
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
84 --l_rtrangeMax=$Library.l_filters.l_rtrange_cond.l_rtrangeMax
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
85 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
86
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
87 #if $Query.q_filters.q_accessions_cond.q_accessions_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
88 --q_accessions=$Query.q_filters.q_accessions_cond.q_accessions
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
89 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
90
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
91 #if $Library.l_filters.l_accessions_cond.l_accessions_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
92 --l_accessions=$Library.l_filters.l_accessions_cond.l_accessions
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
93 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
94
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
95
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
96 #if $Query.q_filters.q_sources_cond.q_sources_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
97 --q_sources=$Query.q_filters.q_sources_cond.q_sources
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
98 --q_sourcesUser='$Query.q_filters.q_sources_cond.q_sourcesUser'
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
99 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
100
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
101 #if $Library.l_filters.l_sources_cond.l_sources_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
102 --l_sources=$Library.l_filters.l_sources_cond.l_sources
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
103 --l_sourcesUser='$Library.l_filters.l_sources_cond.l_sourcesUser'
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
104 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
105
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
106 #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
107 --q_instrumentTypes='$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes'
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
108 --q_instrumentTypesUser='$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser'
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
109 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
110
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
111 #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
112 --l_instrumentTypes='$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes'
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
113 --l_instrumentTypesUser='$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser'
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
114 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
115
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
116 #if $Query.q_filters.q_instruments_cond.q_instruments_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
117 --q_instruments=$Query.q_filters.q_instruments_cond.q_instruments
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
118 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
119
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
120 #if $Library.l_filters.l_instruments_cond.l_instruments_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
121 --l_instruments='$Library.l_filters.l_instruments_cond.l_instruments'
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
122 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
123
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
124 #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
125 --q_spectraTypes=$Query.q_filters.q_spectraTypes_cond.q_spectraTypes
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
126 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
127
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
128 #if $Library.l_filters.l_spectraTypes_cond.l_spectraTypes_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
129 --l_spectraTypes=$Library.l_filters.l_spectraTypes_cond.l_spectraTypes
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
130 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
131
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
132 #if $Query.q_filters.q_spectraFilter
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
133 --q_spectraFilter
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
134 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
135
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
136 #if $Library.l_filters.l_spectraFilter
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
137 --l_spectraFilter
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
138 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
139
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
140 #if $General.rttol_cond.rttol_bool
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
141 --rttol=$General.rttol_cond.rttol
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
142 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
143
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
144 --raW=$General.raW
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
145 --mzW=$General.mzW
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
146
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
147 #if $General.updateDb_cond.updateDb
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
148 --updateDb
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
149 #if $General.updateDb_cond.copyDb
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
150 --copyDb
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
151 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
152 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
153
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
154 #if $General.usePrecursors
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
155 --usePrecursors
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
156 #end if
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
157
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
158 ]]></command>
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
159 <inputs>
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
160 <section name="Query" title="Query spectra input and filters" expanded="True">
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
161 <expand macro="sm_input" ql="Query" ql_shrt = "q" user="True" mspuritydatalib="False" msp="False"
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
162 help="Query SQLite database - in the standard XCMS msPurity workflow - the output
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
163 of msPurity.createDatabase should be used here. However any SQLite database
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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"/>
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
165 <expand macro="filters" ql="Query" ql_shrt="q"/>
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
166 </section>
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
167 <section name="Library" title="Library spectra input and filters" expanded="True">
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
168 <expand macro="sm_input" ql="Library" ql_shrt = "l" user="False" mspuritydatalib="True" msp="False"
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
169 help="Library SQLite database - in the standard XCMS msPurity workflow - a default
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170 database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite
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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"/>
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172 <expand macro="filters" ql="Library" ql_shrt="l"/>
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173 </section>
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174 <section name="General" title="General arguments" expanded="False">
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175 <conditional name="rttol_cond">
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176 <param name="rttol_bool" type="boolean" label="Filter on retention time match?"
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177 help="" />
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178 <when value="true">
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179 <param name="rttol" type="float" value="30" min="0"
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180 label="Retention time tolerance (seconds)"
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181 help="Retention time tolerance in seconds to match precursors"/>
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182 </when>
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183 <when value="false"/>
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184 </conditional>
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185 <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?"
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186 help="If True, spectra will be filtered by similarity of precursors based on
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187 the library and query ppm defined tolerance" />
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188 <param name="raW" label="Weighting for relative abundance" type="float" value="0.5"
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189 help="Relative abundance weight for spectra (default to 0.5 as determined by
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190 massbank for ESI data)"/>
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191 <param name="mzW" label="Weighting for mz" type="float" min="0" value="2"
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192 help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/>
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193 <conditional name="updateDb_cond">
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194 <param name="updateDb" type="boolean" checked="true"
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195 label="Update database with results?" help="" />
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196 <when value="true">
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197 <param name="copyDb" type="boolean" checked="true"
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198 label="Make a copy of the database?"
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199 help="A copy will be made of the input SQLite target database and the
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200 results will be added to this copy. When False, the input SQLite
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201 database will be updated with the matching results. Use False if
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202 you want to reduce storage space being used."/>
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203 </when>
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204 <when value="false"/>
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205 </conditional>
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206 </section>
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207 </inputs>
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208
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209 <outputs>
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210 <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results"
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211 from_work_dir="db_with_spectral_matching.sqlite" >
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212 <filter>create_new_database is True</filter>
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213 </data>
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214 <data name="matches" format="tsv" label="${tool.name} on ${on_string}: matches"
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215 from_work_dir="matched_results.tsv" >
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216 <filter>spectra_type_q == "scans"</filter>
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217 </data>
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218 <data name="xcms_matches" format="tsv" label="${tool.name} on ${on_string}: XCMS matches"
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219 from_work_dir="xcms_matched_results.tsv" />
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220 </outputs>
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221 <tests>
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222 <test>
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223 <param name="q_dbPth" value="createDatabase_output.sqlite" />
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224 <param name="l_dbPth_select" value="userdb" />
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225 <param name="l_dbPth" value="PR100037.sqlite" />
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226 <param name="q_xcmsGroups_bool" value="true" />
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227 <param name="l_accessions_bool" value="true" />
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228 <param name="q_xcmsGroups" value="14" />
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229 <param name="l_accessions" value="PR100037" />
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230 <output name="xcms_matches" file="spectralMatching_matched_results.tsv" />
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231 <output name="matches" file="spectralMatching_xcms_matched_results.tsv" />
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232 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/>
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233 </test>
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234 <test>
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235 <param name="l_instrumentTypes_bool" value="true" />
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236 <param name="q_dbPth" value="createDatabase_output.sqlite" />
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237 <param name="l_dbPth_select" value="userdb" />
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238 <param name="l_dbPth" value="PR100037.sqlite" />
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239 <param name="q_xcmsGroups_bool" value="true" />
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240 <param name="l_accessions_bool" value="true" />
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241 <param name="q_xcmsGroups" value="14" />
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242 <param name="l_accessions" value="PR100037" />
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243 <output name="xcms_matches" file="spectralMatching_matched_results_instrumentTypes.tsv" />
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244 <output name="matches" file="spectralMatching_xcms_matched_results_instrumentTypes.tsv" />
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245 <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite" ftype="sqlite" compare="sim_size"/>
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246 </test>
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247 </tests>
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248
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249 <help><![CDATA[
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250
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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251 =============================================================
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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252 Spectral matching
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253 =============================================================
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254 -----------
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255 General
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256 -----------
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257
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258
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259 Perform spectral matching to spectral libraries for an LC-MS/MS dataset.
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260
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261 The spectral matching is performed from a **Query** SQLite spectral-database against a **Library** SQLite spectral-database.
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262
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263 The SQLite schema of the spectral database here: spectral_database_schema_
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264
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265
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266 The query spectral-database in most cases should contain be the "unknown" spectra database generated the msPurity
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267 function createDatabase as part of a msPurity-XCMS data processing workflow.
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268
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269 The library spectral-database in most cases should contain the "known" spectra from either public or user generated resources.
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270 The library SQLite database by default contains data from MoNA including Massbank, HMDB, LipidBlast and GNPS.
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271 A larger_database_ can be download and used from the msp2db github repository.
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272
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273 To create a user generated library SQLite database the following tool can be used to generate a SQLite database
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274 from a collection of MSP files: msp2db_.
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275
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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
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277 for either the library or query - even allowing for the same database to be used.
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278
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279 The spectral matching functionality has four main components, spectral filtering, spectral alignment, spectral matching,
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280 and summarising the results.
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281
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282 Spectral filtering is simply filtering both the library and query spectra to be search against (e.g. choosing
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283 the library source, instrument, retention time, precursor PPM tolerance etc).
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284
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285 The spectral alignment stage involves aligning the query peaks to the library peaks. The approach used is similar
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286 to modified pMatch algorithm described in Zhou et al 2015.
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287
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288 The spectral matching of the aligned spectra is performed against a combined intensity and m/z weighted vector - created for both
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289 the query and library spectra (wq and wl). See below:
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290
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291 .. math::
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292
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293 w=intensity^x \cdot mz^y
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294
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295
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296 Where x and y represent weight factors and can be adjusted with the parameters raW and mzW.
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297 Defaults to x=0.5 and y=2 as per MassBank for ESI based mass spectrometry data.
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298
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299 The aligned weighted vectors are then matched using dot product cosine, reverse dot product cosine and the composite dot product.
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300 See below for dot product cosine equation.
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301
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302 .. math::
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303
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304 dpc = \frac{ w_q \cdot w_l } { \sqrt{Σ{w_{q}{}^2} } \cdot \sqrt{Σ{w_{l}{}^2}}}
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305
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306
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307 Full details of the matching approaches are described in the msPurity_spectral_matching_vignette_
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308
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309 --------------------------------------------
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310 Example LC-MS/MS processing workflow
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311 --------------------------------------------
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312
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313 * Purity assessments
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314 + (mzML files) -> purityA -> (pa)
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315 * XCMS processing
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316 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
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317 * Fragmentation processing
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318 + (xset, pa) -> frag4feature -> filterFragSpectra -> averageAllFragSpectra -> createDatabase -> **spectralMatching** -> (sqlite spectral database)
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319
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320 -----------
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321 Output
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322 -----------
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323
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324 **Database**
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325
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326 The updated query database (this will have been updated with the annotation results if updateDb argument used)
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327
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328
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329 **xcmsMatchedResults**
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330
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331 If the qeury spectra had XCMS based chromotographic peaks tables (e.g c_peak_groups, c_peaks) in the sqlite database - it will
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332 be possible to summarise the matches for each XCMS grouped feature. The dataframe contains the following columns
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333
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334 * lpid - id in database of library spectra
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335 * qpid - id in database of query spectra
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336 * dpc - dot product cosine of the match
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337 * rdpc - reverse dot product cosine of the match
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338 * cdpc - composite dot product cosine of the match
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339 * mcount - number of matching peaks
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340 * allcount - total number of peaks across both query and library spectra
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341 * mpercent - percentage of matching peaks across both query and library spectra
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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342 * library_rt - retention time of library spectra
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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343 * query_rt - retention time of query spectra
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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344 * rtdiff - difference between library and query retention time
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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345 * library_precursor_mz - library precursor mz
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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346 * query_precursor_mz - query precursor mz
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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347 * library_precursor_ion_purity - library precursor ion purity
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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348 * query_precursor_ion_purity - query precursor ion purity
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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349 * library_accession - library accession value (unique string or number given to eith MoNA or Massbank data entires)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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350 * library_precursor_type - library precursor type (i.e. adduct)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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351 * library_entry_name - Name given to the library spectra
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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352 * inchikey - inchikey of the matched library spectra
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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353 * library_source_name - source of the spectra (e.g. massbank, gnps)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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354 * library_compound_name - name of compound spectra was obtained from
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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355
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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356 **matchedResults**
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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357
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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358 All matched results from the query spectra to the library spectra. Contains the same as above
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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359 without the XCMS details. This table is useful to observe spectral matching results
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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360 for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features.
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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361
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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362
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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363 .. _spectral_database_schema: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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364 .. _larger_database: https://github.com/computational-metabolomics/msp2db/releases
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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365 .. _msp2db: https://github.com/computational-metabolomics/msp2db/releases
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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366 .. _msPurity_spectral_matching_vignette: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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367
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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368 ]]></help>
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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369
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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370 <expand macro="citations"> </expand>
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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371 </tool>