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comparison MS/query_mass_repos.xml @ 6:4393f982d18f

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reorganized sources
author pieter.lukasse@wur.nl
date Thu, 19 Mar 2015 12:22:23 +0100
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5:41f122255d14 6:4393f982d18f
1 <tool id="query_mass_repos"
2 name="METEXP - Find elemental composition formulas based on mass values "
3 version="0.1.0">
4 <description>Query multiple public repositories for elemental compositions from accurate mass values detected by high-resolution mass spectrometers</description>
5 <command interpreter="python">
6 query_mass_repos.py
7 $input_file
8 "$molecular_mass_col"
9 "$repository_file"
10 $error_margin
11 $margin_unit
12 $output_result
13 </command>
14 <inputs>
15
16 <param name="input_file" format="tabular" type="data"
17 label="Input file"
18 help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/>
19
20 <param name="molecular_mass_col" type="text" size="50"
21 label="Molecular mass column name"
22 value="MM"
23 help="Name of the column containing the molecular mass information (in the given input file)" />
24
25 <param name="repository_file" type="select" label="Repository/service to query"
26 help="Select the repository/service which should be queried"
27 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_MassSearch_Services")'/>
28
29 <param name="error_margin" type="float" size="10"
30 label="Error marging"
31 value="0.01"
32 help="Mass difference allowed when searching in the repositories for a mass match." />
33
34 <param name="margin_unit" type="select" label="Margin unit">
35 <option value="ms" selected="True">ms</option>
36 <option value="ppm">ppm</option>
37 </param>
38 <!-- TODO
39 <param name="metexp_access_key" type="text" size="50"
40 label="(Optional)MetExp access key"
41 value=""
42 help="Key needed to get access to MetExp services. Fill in if MetExp service was selected" /> -->
43
44 </inputs>
45 <outputs>
46 <data name="output_result" format="tabular" label="${tool.name} on ${on_string}" />
47 </outputs>
48 <code file="match_library.py" /> <!-- file containing get_directory_files function used above-->
49 <help>
50 .. class:: infomark
51
52 This tool will query multiple public repositories such as PRI-MetExp or http://webs2.kazusa.or.jp/mfsearcher
53 for elemental compositions from accurate mass values detected by high-resolution mass spectrometers.
54
55 It will take the input file and for each record it will query the
56 molecular mass in the selected repository. If one or more compounds are found in the
57 repository then extra information regarding (mass based)matching elemental composition formulas is added to the output file.
58
59 The output file is thus the input file enriched with information about
60 related items found in the selected repository.
61
62 **Notes**
63
64 The input file can be any tabular file, as long as it contains a column for the molecular mass.
65
66 **Services that can be queried**
67
68 ================= =========================================================================
69 Database Description
70 ----------------- -------------------------------------------------------------------------
71 PRI-MetExp LC-MS and GC-MS data from experiments from the metabolomics group at
72 Plant Research International. NB: restricted access to employees with
73 access key.
74 ExactMassDB A database of possible elemental compositions consits of C: 100,
75 H: 200, O: 50, N: 10, P: 10, and S: 10, that satisfy the Senior and
76 the Lewis valence rules.
77 (via /mfsearcher/exmassdb/)
78 ExactMassDB-HR2 HR2, which is one of the fastest tools for calculation of elemental
79 compositions, filters some elemental compositions according to
80 the Seven Golden Rules (Kind and Fiehn, 2007). The ExactMassDB-HR2
81 database returns the same result as does HR2 with the same atom kind
82 and number condition as that used in construction of the ExactMassDB.
83 (via /mfsearcher/exmassdb-hr2/)
84 Pep1000 A database of possible linear polypeptides that are
85 constructed with 20 kinds of amino acids and having molecular
86 weights smaller than 1000.
87 (via /mfsearcher/pep1000/)
88 KEGG Re-calculated compound data from KEGG. Weekly updated.
89 (via /mfsearcher/kegg/)
90 KNApSAcK Re-calculated compound data from KNApSAcK.
91 (via /mfsearcher/knapsack/)
92 Flavonoid Viewer Re-calculated compound data from Flavonoid Viewer .
93 (via /mfsearcher/flavonoidviewer/
94 LipidMAPS Re-calculated compound data from LIPID MAPS.
95 (via /mfsearcher/lipidmaps/)
96 HMDB Re-calculated compound data from Human Metabolome Database (HMDB)
97 Version 3.5.
98 (via /mfsearcher/hmdb/)
99 PubChem Re-calculated compound data from PubChem. Monthly updated.
100 (via /mfsearcher/pubchem/)
101 ================= =========================================================================
102
103 Sources for table above: PRI-MetExp and http://webs2.kazusa.or.jp/mfsearcher
104
105 </help>
106 </tool>