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comparison filterFragSpectra.xml @ 0:d6321d0e6efe draft

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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 08:54:42 -0400
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1 <tool id="mspurity_filterfragspectra" name="msPurity.filterFragSpectra" version="0.2.0">
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 </expand>
10 <stdio>
11 <exit_code range="1:" />
12 </stdio>
13 <command interpreter="Rscript"><![CDATA[
14 filterFragSpectra.R
15 --out_rdata=$filterFragSpectra_output_rdata
16 --out_peaklist_prec=$filterFragSpectra_output_prec_tsv
17 --out_peaklist_frag=$filterFragSpectra_output_frag_tsv
18 --pa="$pa"
19 --ilim=$ilim
20 --plim=$plim
21 --ra=$ra
22 --snr=$snr
23 --snmeth=$snmeth
24 $rmp
25 ]]></command>
26 <inputs>
27 <param name="pa" type="data"
28 label="purityA object with fragmentation linked to XCMS features" format="rdata"
29 help="purityA object saved as 'pa' in a RData file where fragmentation has
30 been linked to XCMS features(output from frag4feature tool)"/>
31 <param name="plim" type="float" value="0.5" help=""
32 label="Miniumum precursor ion purity of the associated precursor for
33 fragmentation spectra scan" />
34 <param name="ilim" type="float" value="0.0" label="Peak instensity threshold" help="" />
35 <param name="ra" type="float" min="0.0" max="1.0" value="0.0"
36 label="Relative abundance threshold" help="" />
37 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold" help="" />
38 <param name="snmeth" type="select" label="Function to calculate noise." help="" >
39 <option value="median" selected="true">median</option>
40 <option value="mean">mean</option>
41 <!-- <option value="mad">mad</option> -->
42 </param>
43 <param name="rmp" type="boolean" checked="false" truevalue="--remove_peaks" falsevalue=""
44 label="Remove peaks that do not meet the filtering criteria.
45 Otherwise peaks will be flagged instead."
46 help="" />
47 </inputs>
48 <outputs>
49 <data name="filterFragSpectra_output_rdata" format="rdata"
50 label="${tool.name} on ${on_string}: RData" />
51 <data name="filterFragSpectra_output_prec_tsv" format="tsv"
52 label="${tool.name} on ${on_string}: peaklist (precursors)" />
53 <data name="filterFragSpectra_output_frag_tsv" format="tsv"
54 label="${tool.name} on ${on_string}: peaklist (fragments)" />
55 </outputs>
56 <tests>
57 <test>
58 <param name="pa" value="frag4feature_output.RData" />
59 <output name="filterFragSpectra_output_rdata"
60 file="filterFragSpectra_output.RData" ftype="rdata" compare="sim_size" />
61 <output name="filterFragSpectra_output_prec_tsv"
62 file="filterFragSpectra_output_prec.tsv" ftype="tsv" />
63 <output name="filterFragSpectra_output_frag_tsv"
64 file="filterFragSpectra_output_frag.tsv" ftype="tsv" />
65 </test>
66 </tests>
67
68 <help><![CDATA[
69 =============================================================
70 Filter Fragmentation Spectra
71 =============================================================
72 -----------
73 Description
74 -----------
75
76 Tool to .
77
78
79 The data inputs are:
80
81 *
82
83 See Bioconductor documentation for more details, functions:
84 msPurity::filterFragSpectra()
85
86 -----------
87 Outputs
88 -----------
89 * filter_fragmentation_spectra_rdata
90 * peaklist_prec_tsv
91 * peaklist_frag_tsv
92
93 ]]></help>
94
95 <expand macro="citations" />
96
97 </tool>