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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 08:57:02 -0400
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-1:000000000000 0:b82a7c818839
1 <tool id="mspurity_averagefragspectra" name="msPurity.averageFragSpectra" version="0.2.0">
2 <description>
3 Average and filter LC-MS/MS fragmentation spectra (Inter, Intra or All)
4 </description>
5
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9
10 <expand macro="requirements">
11 </expand>
12
13 <stdio>
14 <exit_code range="1:" />
15 </stdio>
16 <command interpreter="Rscript"><![CDATA[
17 averageFragSpectra.R
18 --out_rdata="$averageFragSpectra_output_rdata"
19 --out_peaklist="$averageFragSpectra_output_tsv"
20 --pa="$pa"
21 --av_level=$av_level
22 --cores=\${GALAXY_SLOTS:-4}
23 --minfrac=$minfrac
24 --minnum=$minnum
25 --ppm=$ppm
26 --snr=$snr
27 --ra=$ra
28 --av=$av
29 $sumi
30 $rmp
31 ]]></command>
32 <inputs>
33 <param name="pa" type="data" label="purityA object" format="rdata"
34 help="purityA object saved as 'pa' in a RData file (output from frag4feature tool)"/>
35
36 <conditional name="av">
37 <param name="level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
38 <option value="intra" selected="true">within a MS data file</option>
39 <option value="inter">accross MS data files</option>
40 <option value="all">within and accross MS data files (ignoring intra and inter relationships)</option>
41 </param>
42 <when value="intra">
43 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
44 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
45 </when>
46 <when value="inter">
47 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
48 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
49 </when>
50 <when value="all">
51 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
52 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
53 </when>
54 </conditional>
55
56 <param name="av_level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
57 <option value="intra" selected="true">within a MS data file</option>
58 <option value="inter">accross MS data files</option>
59 <option value="all">within and accross MS data files (ignoring intra and inter relationships)</option>
60 </param>
61 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
62 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
63 <param name="minfrac" type="float" min="0.0" max="1.0" value="0.5" label="Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in." help="" />
64 <param name="minnum" type="integer" value="1" label="Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor)." help="" />
65 <param name="ppm" type="float" value="5.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in parts per million." />
66 <param name="sumi" type="boolean" checked="false" truevalue="--sumi" falsevalue="" label="Sum intensities across (averaged) scans?" help="" />
67 <param name="av" type="select" label="Function to calculate the average intensity, m/z and SNR values across (averaged) scans after filtering." help="This is ignored for intensities when intensities are summed." >
68 <option value="median" selected="true">median</option>
69 <option value="mean">mean</option>
70 </param>
71
72 <param name="rmp" type="boolean" checked="true" truevalue="--rmp" falsevalue="" label="Remove peaks that do not meet the filtering criteria. Otherwise peaks will be flagged instead."
73 help="" />
74 </inputs>
75 <outputs>
76 <data name="averageFragSpectra_output_rdata" format="rdata" label="${tool.name} (${av_level}) on ${on_string}: RData" />
77 <data name="averageFragSpectra_output_tsv" format="tsv" label="${tool.name} (${av_level}) on ${on_string}: peaklist" />
78 </outputs>
79 <tests>
80 <test>
81 <param name="av_level" value="intra" />
82 <param name="pa" value="filterFragSpectra_output.RData" />
83 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_intra.RData" ftype="rdata" compare="sim_size" />
84 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_intra.tsv" ftype="tsv" />
85 </test>
86 <test>
87 <param name="av_level" value="inter" />
88 <param name="pa" value="averageFragSpectra_output_intra.RData" />
89 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_inter.RData" ftype="rdata" compare="sim_size" />
90 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_inter.tsv" ftype="tsv" />
91 </test>
92 <test>
93 <param name="av_level" value="all" />
94 <param name="pa" value="frag4feature_output.RData" />
95 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_all_only.RData" ftype="rdata" compare="sim_size" />
96 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_all_only.tsv" ftype="tsv" />
97 </test>
98 <test>
99 <param name="av_level" value="all" />
100 <param name="pa" value="averageFragSpectra_output_inter.RData" />
101 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_all.RData" ftype="rdata" compare="sim_size" />
102 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_all.tsv" ftype="tsv" />
103
104 </test>
105 </tests>
106
107 <help><![CDATA[
108 =============================================================
109 Average Fragmentation Spectra
110 =============================================================
111 -----------
112 Description
113 -----------
114
115 Average and filter fragmentation spectra for each XCMS feature using an msPurity purityA object.
116
117 The tool uses the msPurity functions averageAllFragSpectra, averageIntraFragSpectra and
118 averageInterFragSpectra.
119
120 The fragmentation spectra can be averaged in multiple ways; intra will average fragmentation
121 spectra within an mzML file, inter will average fragmentation spectra across mzML files
122 (requires intra to be run first) and all will average all spectra ignoring the intra and
123 inter relationships.
124
125 The averaging is performed using hierarchical clustering of the m/z values of each peaks,
126 where m/z values within a set ppm tolerance will be clustered. The clustered peaks are then
127 averaged (or summed).
128
129 The fragmentation can be filtered on the averaged spectra (with the arguments snr, rsd, minfrac, ra)
130
131
132 See Bioconductor documentation for more details, functions:
133 msPurity::averageIntraFragSpectra()
134 msPurity::averageInterFragSpectra()
135 msPurity::averageAllFragSpectra()
136
137 -----------
138 Outputs
139 -----------
140 * average_x_fragmentation_spectra_rdata
141
142 ]]></help>
143
144 <expand macro="citations" />
145
146 </tool>