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annotate query_mass_repos.xml @ 40:a7b609941846

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author pieter.lukasse@wur.nl
date Fri, 19 Sep 2014 16:14:58 +0200
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1 <tool id="query_mass_repos"
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2 name="METEXP - Find elemental composition formulas based on mass values "
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3 version="0.1.0">
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4 <description>Query multiple public repositories for elemental compositions from accurate mass values detected by high-resolution mass spectrometers</description>
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5 <command interpreter="python">
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6 query_mass_repos.py
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7 $input_file
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8 "$molecular_mass_col"
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9 "$repository_file"
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10 $error_margin
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11 $margin_unit
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12 $output_result
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13 </command>
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14 <inputs>
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15
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16 <param name="input_file" format="tabular" type="data"
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17 label="Input file"
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18 help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/>
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19
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20 <param name="molecular_mass_col" type="text" size="50"
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21 label="Molecular mass column name"
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22 value="MM"
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23 help="Name of the column containing the molecular mass information (in the given input file)" />
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24
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25 <param name="repository_file" type="select" label="Repository/service to query"
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26 help="Select the repository/service which should be queried"
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27 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_MassSearch_Services")'/>
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28
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29 <param name="error_margin" type="float" size="10"
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30 label="Error marging"
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31 value="0.01"
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32 help="Mass difference allowed when searching in the repositories for a mass match." />
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33
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34 <param name="margin_unit" type="select" label="Margin unit">
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35 <option value="ms" selected="True">ms</option>
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36 <option value="ppm">ppm</option>
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37 </param>
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38 <!-- TODO
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39 <param name="metexp_access_key" type="text" size="50"
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40 label="(Optional)MetExp access key"
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41 value=""
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42 help="Key needed to get access to MetExp services. Fill in if MetExp service was selected" /> -->
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44 </inputs>
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45 <outputs>
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46 <data name="output_result" format="tabular" label="${tool.name} on ${on_string}" />
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47 </outputs>
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48 <code file="match_library.py" /> <!-- file containing get_directory_files function used above-->
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49 <help>
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50 .. class:: infomark
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51
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52 This tool will query multiple public repositories such as PRI-MetExp or http://webs2.kazusa.or.jp/mfsearcher
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53 for elemental compositions from accurate mass values detected by high-resolution mass spectrometers.
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54
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55 It will take the input file and for each record it will query the
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56 molecular mass in the selected repository. If one or more compounds are found in the
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57 repository then extra information regarding (mass based)matching elemental composition formulas is added to the output file.
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58
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59 The output file is thus the input file enriched with information about
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60 related items found in the selected repository.
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61
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62 **Notes**
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63
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64 The input file can be any tabular file, as long as it contains a column for the molecular mass.
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65
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66 **Services that can be queried**
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67
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68 ================= =========================================================================
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69 Database Description
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70 ----------------- -------------------------------------------------------------------------
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71 PRI-MetExp LC-MS and GC-MS data from experiments from the metabolomics group at
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72 Plant Research International. NB: restricted access to employees with
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73 access key.
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74 ExactMassDB A database of possible elemental compositions consits of C: 100,
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75 H: 200, O: 50, N: 10, P: 10, and S: 10, that satisfy the Senior and
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76 the Lewis valence rules.
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77 (via /mfsearcher/exmassdb/)
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78 ExactMassDB-HR2 HR2, which is one of the fastest tools for calculation of elemental
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79 compositions, filters some elemental compositions according to
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80 the Seven Golden Rules (Kind and Fiehn, 2007). The ExactMassDB-HR2
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81 database returns the same result as does HR2 with the same atom kind
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82 and number condition as that used in construction of the ExactMassDB.
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83 (via /mfsearcher/exmassdb-hr2/)
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84 Pep1000 A database of possible linear polypeptides that are
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85 constructed with 20 kinds of amino acids and having molecular
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86 weights smaller than 1000.
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87 (via /mfsearcher/pep1000/)
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88 KEGG Re-calculated compound data from KEGG. Weekly updated.
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89 (via /mfsearcher/kegg/)
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90 KNApSAcK Re-calculated compound data from KNApSAcK.
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91 (via /mfsearcher/knapsack/)
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92 Flavonoid Viewer Re-calculated compound data from Flavonoid Viewer .
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93 (via /mfsearcher/flavonoidviewer/
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94 LipidMAPS Re-calculated compound data from LIPID MAPS.
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95 (via /mfsearcher/lipidmaps/)
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96 HMDB Re-calculated compound data from Human Metabolome Database (HMDB)
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97 Version 3.5.
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98 (via /mfsearcher/hmdb/)
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99 PubChem Re-calculated compound data from PubChem. Monthly updated.
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100 (via /mfsearcher/pubchem/)
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101 ================= =========================================================================
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102
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103 Sources for table above: PRI-MetExp and http://webs2.kazusa.or.jp/mfsearcher
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104
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105 </help>
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106 </tool>