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comparison query_metexp.xml @ 30:60b53f2aa48a

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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-->