Mercurial > repos > pieterlukasse > prims_metabolomics
comparison query_metexp.xml @ 21:19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
* Improved quantification output files of MsClust, a.o. sorting
mass list based on intensity (last two columns of quantification
files)
* Added Molecular Mass calculation method
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 05 Mar 2014 17:20:11 +0100 |
| parents | |
| children | ab7f9ec70ffc |
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| 20:24fb75fedee0 | 21:19d8fd10248e |
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| 1 <tool id="query_metexp" | |
| 2 name="METEXP - Query Database " | |
| 3 version="0.1.0"> | |
| 4 <description>Query a set of identifications against the METabolomics EXPlorer database</description> | |
| 5 <command interpreter="python"> | |
| 6 query_metexp.py | |
| 7 $input_file | |
| 8 $casid_col | |
| 9 $formula_col | |
| 10 $molecular_mass_col | |
| 11 "$metexp_dblink_file" | |
| 12 $separation_method | |
| 13 $output_result | |
| 14 </command> | |
| 15 <inputs> | |
| 16 | |
| 17 <param name="input_file" format="tabular" type="data" | |
| 18 label="Input file" | |
| 19 help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/> | |
| 20 | |
| 21 <param name="casid_col" type="text" size="50" | |
| 22 label="CAS ID column name" | |
| 23 value="CAS" | |
| 24 help="Name of the column containing the CAS code information (in the given input file)" /> | |
| 25 <param name="formula_col" type="text" size="50" | |
| 26 label="Formula ID column name" | |
| 27 value="FORMULA" | |
| 28 help="Name of the column containing the formula information (in the given input file)" /> | |
| 29 <param name="molecular_mass_col" type="text" size="50" | |
| 30 label="Molecular mass column name" | |
| 31 value="MM" | |
| 32 help="Name of the column containing the molecular mass information (in the given input file)" /> | |
| 33 | |
| 34 <param name="metexp_dblink_file" type="select" label="MetExp DB to query" | |
| 35 help="Select the MetExp Database/backend which should be queried" | |
| 36 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_Databases")'/> | |
| 37 | |
| 38 <param name="separation_method" type="select" label="Data type to query"> | |
| 39 <option value="GC" selected="True">GC</option> | |
| 40 <option value="LC">LC</option> | |
| 41 </param> | |
| 42 | |
| 43 </inputs> | |
| 44 <outputs> | |
| 45 <data name="output_result" format="tabular" label="${tool.name} on ${on_string}" /> | |
| 46 </outputs> | |
| 47 <code file="match_library.py" /> <!-- file containing get_directory_files function used above--> | |
| 48 <help> | |
| 49 .. class:: infomark | |
| 50 | |
| 51 This tool will Query a set of identifications against the METabolomics EXPlorer database. | |
| 52 | |
| 53 It will take the input file and for each record it will query the | |
| 54 molecular mass in the selected MetExp DB. If one or more compounds are found in the | |
| 55 MetExp DB then extra information regarding these compounds is added to the output file. | |
| 56 | |
| 57 The output file is thus the input file enriched with information about | |
| 58 related items found in the selected MetExp DB. | |
| 59 | |
| 60 **Notes** | |
| 61 | |
| 62 The input file can be any tabular file, as long as it contains a column for the molecular mass | |
| 63 and one for the formula of the respective identification. | |
| 64 | |
| 65 | |
| 66 </help> | |
| 67 </tool> |