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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:15:17 +0000
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1 <tool id="mspurity_filterfragspectra" name="msPurity.filterFragSpectra" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description>
3 Filter fragmentations spectra associated with an XCMS feature
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <command detect_errors="exit_code" interpreter="Rscript"><![CDATA[
10 filterFragSpectra.R
11 --out_rdata='$filterFragSpectra_output_rdata'
12 --out_peaklist_prec='$filterFragSpectra_output_prec_tsv'
13 --out_peaklist_frag='$filterFragSpectra_output_frag_tsv'
14 --pa='$pa'
15 --ilim=$ilim
16 --plim=$plim
17 --ra=$ra
18 --snr=$snr
19 --snmeth=$snmeth
20 $rmp
21 ]]></command>
22 <inputs>
23 <param argument="--pa" type="data"
24 label="purityA object with fragmentation linked to XCMS features" format="rdata"
25 help="purityA object saved as 'pa' in a RData file where fragmentation has
26 been linked to XCMS features(output from frag4feature tool)"/>
27 <param argument="--plim" type="float" value="0.5" help=""
28 label="Miniumum precursor ion purity of the associated precursor for
29 fragmentation spectra scan" />
30 <param argument="--ilim" type="float" value="0.0" label="Peak instensity threshold" help="" />
31 <param argument="--ra" type="float" min="0.0" max="1.0" value="0.0"
32 label="Relative abundance threshold" help="" />
33 <param argument="--snr" type="float" value="0.0" label="Signal-to-noise threshold" help="" />
34 <param argument="--snmeth" type="select" label="Function to calculate noise." help="" >
35 <option value="median" selected="true">median</option>
36 <option value="mean">mean</option>
37 <!-- <option value="mad">mad</option> -->
38 </param>
39 <param argument="--rmp" type="boolean" checked="false" truevalue="--rmp" falsevalue=""
40 label="Remove peaks that do not meet the filtering criteria.
41 Otherwise peaks will be flagged instead."
42 help="" />
43 </inputs>
44 <outputs>
45 <data name="filterFragSpectra_output_rdata" format="rdata"
46 label="${tool.name} on ${on_string}: RData" />
47 <data name="filterFragSpectra_output_prec_tsv" format="tsv"
48 label="${tool.name} on ${on_string}: peaklist (precursors)" />
49 <data name="filterFragSpectra_output_frag_tsv" format="tsv"
50 label="${tool.name} on ${on_string}: peaklist (fragments)" />
51 </outputs>
52 <tests>
53 <test>
54 <param name="pa" value="frag4feature_output.RData" />
55 <output name="filterFragSpectra_output_rdata"
56 file="filterFragSpectra_output.RData" ftype="rdata" compare="sim_size" />
57 <output name="filterFragSpectra_output_prec_tsv"
58 file="filterFragSpectra_output_prec.tsv" ftype="tsv" />
59 <output name="filterFragSpectra_output_frag_tsv"
60 file="filterFragSpectra_output_frag.tsv" ftype="tsv" />
61 </test>
62 </tests>
63
64 <help><![CDATA[
65 =============================================================
66 Filter Fragmentation Spectra
67 =============================================================
68 -----------
69 Description
70 -----------
71
72 Flag and filter features based on signal-to-noise ratio, relative abundance, intensity threshold and precursor ion purity of precursor.
73
74
75 **Example LC-MS/MS processing workflow**
76
77
78 * Purity assessments
79 + (mzML files) -> purityA -> (pa)
80 * XCMS processing
81 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
82 * Fragmentation processing
83 + (xset, pa) -> frag4feature -> **filterFragSpectra** -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)
84
85 See Bioconductor documentation for more details, functions:
86 msPurity::filterFragSpectra()
87
88 -----------
89 Outputs
90 -----------
91 * filter_fragmentation_spectra_rdata: RData of the purityA object (pa) with filtered data
92 * peaklist_prec_tsv: precursor peaklist
93 * peaklist_frag_tsv: fragmentation peaklist
94
95 ]]></help>
96
97 <expand macro="citations" />
98
99 </tool>