6
+ − 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>
