Mercurial > repos > pieterlukasse > prims_metabolomics2
comparison METEXPtools/query_metexp.xml @ 6:4393f982d18f
reorganized sources
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Thu, 19 Mar 2015 12:22:23 +0100 |
| parents | |
| children | 5a753524e525 |
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| 5:41f122255d14 | 6:4393f982d18f |
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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 EXPeriments 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 $output_result | |
| 14 </command> | |
| 15 <inputs> | |
| 16 | |
| 17 <param name="input_file" format="tabular" type="data" | |
| 18 label="Input file" | |
| 19 help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/> | |
| 20 | |
| 21 <param name="separation_method" type="select" label="Data type to query"> | |
| 22 <option value="GC" selected="True">GC</option> | |
| 23 <option value="LC">LC</option> | |
| 24 </param> | |
| 25 | |
| 26 | |
| 27 <param name="casid_col" type="text" size="50" | |
| 28 label="CAS ID column name" | |
| 29 value="CAS" | |
| 30 help="Name of the column containing the CAS code information (in the given input file)" /> | |
| 31 <param name="formula_col" type="text" size="50" | |
| 32 label="Formula ID column name" | |
| 33 value="FORMULA" | |
| 34 help="Name of the column containing the formula information (in the given input file)" /> | |
| 35 <param name="molecular_mass_col" type="text" size="50" | |
| 36 label="Molecular mass column name" | |
| 37 value="MM" | |
| 38 help="Name of the column containing the molecular mass information (in the given input file)" /> | |
| 39 | |
| 40 <param name="metexp_dblink_file" type="select" label="MetExp DB to query" | |
| 41 help="Select the MetExp Database/backend which should be queried" | |
| 42 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_Databases")'/> | |
| 43 | |
| 44 | |
| 45 </inputs> | |
| 46 <outputs> | |
| 47 <data name="output_result" format="tabular" label="${tool.name} on ${on_string}" /> | |
| 48 </outputs> | |
| 49 <code file="match_library.py" /> <!-- file containing get_directory_files function used above--> | |
| 50 <help> | |
| 51 .. class:: infomark | |
| 52 | |
| 53 This tool will Query a set of identifications against the METabolomics EXPlorer database. | |
| 54 | |
| 55 It will take the input file and for each record it will query the | |
| 56 molecular mass in the selected MetExp DB. If one or more compounds are found in the | |
| 57 MetExp DB then extra information regarding these compounds 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 MetExp DB. | |
| 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 and one for the formula of the respective identification. | |
| 66 | |
| 67 | |
| 68 </help> | |
| 69 </tool> |