Mercurial > repos > pieterlukasse > prims_metabolomics
comparison query_metexp.xml @ 30:60b53f2aa48a
Small fixes, added microminutes support to MsClust, removed TIC or MsClust output
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Sat, 30 Aug 2014 16:14:18 +0200 |
| parents | ab7f9ec70ffc |
| children |
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| 29:0d534bce8e84 | 30:60b53f2aa48a |
|---|---|
| 1 <tool id="query_metexp" | 1 <tool id="query_metexp" |
| 2 name="METEXP - Query Database " | 2 name="METEXP - Query Database " |
| 3 version="0.1.0"> | 3 version="0.1.0"> |
| 4 <description>Query a set of identifications against the METabolomics EXPlorer database</description> | 4 <description>Query a set of identifications against the METabolomics EXPeriments database</description> |
| 5 <command interpreter="python"> | 5 <command interpreter="python"> |
| 6 query_metexp.py | 6 query_metexp.py |
| 7 $input_file | 7 $input_file |
| 8 "$casid_col" | 8 "$casid_col" |
| 9 "$formula_col" | 9 "$formula_col" |
| 15 <inputs> | 15 <inputs> |
| 16 | 16 |
| 17 <param name="input_file" format="tabular" type="data" | 17 <param name="input_file" format="tabular" type="data" |
| 18 label="Input file" | 18 label="Input file" |
| 19 help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/> | 19 help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/> |
| 20 | |
| 21 <param name="separation_method" type="select" label="Data type to query"> | |
| 22 <option value="GC" selected="True">GC</option> | |
| 23 <option value="LC">LC</option> | |
| 24 </param> | |
| 25 | |
| 20 | 26 |
| 21 <param name="casid_col" type="text" size="50" | 27 <param name="casid_col" type="text" size="50" |
| 22 label="CAS ID column name" | 28 label="CAS ID column name" |
| 23 value="CAS" | 29 value="CAS" |
| 24 help="Name of the column containing the CAS code information (in the given input file)" /> | 30 help="Name of the column containing the CAS code information (in the given input file)" /> |
| 33 | 39 |
| 34 <param name="metexp_dblink_file" type="select" label="MetExp DB to query" | 40 <param name="metexp_dblink_file" type="select" label="MetExp DB to query" |
| 35 help="Select the MetExp Database/backend which should be queried" | 41 help="Select the MetExp Database/backend which should be queried" |
| 36 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_Databases")'/> | 42 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_Databases")'/> |
| 37 | 43 |
| 38 <param name="separation_method" type="select" label="Data type to query"> | 44 |
| 39 <option value="GC" selected="True">GC</option> | |
| 40 <option value="LC">LC</option> | |
| 41 </param> | |
| 42 | |
| 43 </inputs> | 45 </inputs> |
| 44 <outputs> | 46 <outputs> |
| 45 <data name="output_result" format="tabular" label="${tool.name} on ${on_string}" /> | 47 <data name="output_result" format="tabular" label="${tool.name} on ${on_string}" /> |
| 46 </outputs> | 48 </outputs> |
| 47 <code file="match_library.py" /> <!-- file containing get_directory_files function used above--> | 49 <code file="match_library.py" /> <!-- file containing get_directory_files function used above--> |