Mercurial > repos > tomnl > mspurity_filterfragspectra

comparison filterFragSpectra.xml @ 1:11f138472bb2 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e67cf7a95ce430d1d373c03992a615da2f3eeeb1
author tomnl
date Tue, 04 Jun 2019 10:32:31 -0400
parents d6321d0e6efe
children 43d4dd3288cd
comparison
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0:d6321d0e6efe 1:11f138472bb2
1 <tool id="mspurity_filterfragspectra" name="msPurity.filterFragSpectra" version="0.2.0"> 1 <tool id="mspurity_filterfragspectra" name="msPurity.filterFragSpectra" version="0.2.1">
2 <description> 2 <description>
3 Filter fragmentations spectra associated with an XCMS feature 3 Filter fragmentations spectra associated with an XCMS feature
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
71 ============================================================= 71 =============================================================
72 ----------- 72 -----------
73 Description 73 Description
74 ----------- 74 -----------
75 75
76 Tool to . 76 Flag and filter features based on signal-to-noise ratio, relative abundance, intensity threshold and precursor ion purity of precursor.
77 77
78 78
79 The data inputs are: 79 **Example LC-MS/MS processing workflow**
80 80
81 * 81
82 * Purity assessments
83 + (mzML files) -> purityA -> (pa)
84 * XCMS processing
85 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
86 * Fragmentation processing
87 + (xset, pa) -> frag4feature -> **filterFragSpectra** -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)
82 88
83 See Bioconductor documentation for more details, functions: 89 See Bioconductor documentation for more details, functions:
84 msPurity::filterFragSpectra() 90 msPurity::filterFragSpectra()
85 91
86 ----------- 92 -----------
87 Outputs 93 Outputs
88 ----------- 94 -----------
89 * filter_fragmentation_spectra_rdata 95 * filter_fragmentation_spectra_rdata: RData of the purityA object (pa) with filtered data
90 * peaklist_prec_tsv 96 * peaklist_prec_tsv: precursor peaklist
91 * peaklist_frag_tsv 97 * peaklist_frag_tsv: fragmentation peaklist
92 98
93 ]]></help> 99 ]]></help>
94 100
95 <expand macro="citations" /> 101 <expand macro="citations" />
96 102