Mercurial > repos > pieterlukasse > prims_metabolomics
view query_mass_repos.xml @ 27:ecd3f6c9e606
small fix to support spaces in parameters
author | pieter.lukasse@wur.nl |
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date | Thu, 01 May 2014 11:19:52 +0200 |
parents | ab7f9ec70ffc |
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<tool id="query_mass_repos" name="METEXP - Find elemental composition formulas based on mass values " version="0.1.0"> <description>Query multiple public repositories for elemental compositions from accurate mass values detected by high-resolution mass spectrometers</description> <command interpreter="python"> query_mass_repos.py $input_file "$molecular_mass_col" "$repository_file" $error_margin $margin_unit $output_result </command> <inputs> <param name="input_file" format="tabular" type="data" label="Input file" help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/> <param name="molecular_mass_col" type="text" size="50" label="Molecular mass column name" value="MM" help="Name of the column containing the molecular mass information (in the given input file)" /> <param name="repository_file" type="select" label="Repository/service to query" help="Select the repository/service which should be queried" dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_MassSearch_Services")'/> <param name="error_margin" type="float" size="10" label="Error marging" value="0.01" help="Mass difference allowed when searching in the repositories for a mass match." /> <param name="margin_unit" type="select" label="Margin unit"> <option value="ms" selected="True">ms</option> <option value="ppm">ppm</option> </param> <!-- TODO <param name="metexp_access_key" type="text" size="50" label="(Optional)MetExp access key" value="" help="Key needed to get access to MetExp services. Fill in if MetExp service was selected" /> --> </inputs> <outputs> <data name="output_result" format="tabular" label="${tool.name} on ${on_string}" /> </outputs> <code file="match_library.py" /> <!-- file containing get_directory_files function used above--> <help> .. class:: infomark This tool will query multiple public repositories such as PRI-MetExp or http://webs2.kazusa.or.jp/mfsearcher for elemental compositions from accurate mass values detected by high-resolution mass spectrometers. It will take the input file and for each record it will query the molecular mass in the selected repository. If one or more compounds are found in the repository then extra information regarding (mass based)matching elemental composition formulas is added to the output file. The output file is thus the input file enriched with information about related items found in the selected repository. **Notes** The input file can be any tabular file, as long as it contains a column for the molecular mass. **Services that can be queried** ================= ========================================================================= Database Description ----------------- ------------------------------------------------------------------------- PRI-MetExp LC-MS and GC-MS data from experiments from the metabolomics group at Plant Research International. NB: restricted access to employees with access key. ExactMassDB A database of possible elemental compositions consits of C: 100, H: 200, O: 50, N: 10, P: 10, and S: 10, that satisfy the Senior and the Lewis valence rules. (via /mfsearcher/exmassdb/) ExactMassDB-HR2 HR2, which is one of the fastest tools for calculation of elemental compositions, filters some elemental compositions according to the Seven Golden Rules (Kind and Fiehn, 2007). The ExactMassDB-HR2 database returns the same result as does HR2 with the same atom kind and number condition as that used in construction of the ExactMassDB. (via /mfsearcher/exmassdb-hr2/) Pep1000 A database of possible linear polypeptides that are constructed with 20 kinds of amino acids and having molecular weights smaller than 1000. (via /mfsearcher/pep1000/) KEGG Re-calculated compound data from KEGG. Weekly updated. (via /mfsearcher/kegg/) KNApSAcK Re-calculated compound data from KNApSAcK. (via /mfsearcher/knapsack/) Flavonoid Viewer Re-calculated compound data from Flavonoid Viewer . (via /mfsearcher/flavonoidviewer/ LipidMAPS Re-calculated compound data from LIPID MAPS. (via /mfsearcher/lipidmaps/) HMDB Re-calculated compound data from Human Metabolome Database (HMDB) Version 3.5. (via /mfsearcher/hmdb/) PubChem Re-calculated compound data from PubChem. Monthly updated. (via /mfsearcher/pubchem/) ================= ========================================================================= Sources for table above: PRI-MetExp and http://webs2.kazusa.or.jp/mfsearcher </help> </tool>