Mercurial > repos > pieterlukasse > prims_metabolomics

comparison export_to_metexp_tabular.xml @ 26:637830ac8bcd

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added validation in metexp to tabular tool; added workaround/fix for L and D compound types
author pieter.lukasse@wur.nl
date Thu, 24 Apr 2014 11:28:38 +0200
parents 19d8fd10248e
children ecd3f6c9e606
comparison
equal deleted inserted replaced
25:ab7f9ec70ffc 26:637830ac8bcd
1 <tool id="export_to_metexp_tabular" 1 <tool id="export_to_metexp_tabular"
2 name="METEXP - Tabular file" 2 name="METEXP - Tabular file"
3 version="0.1.0"> 3 version="0.2.0">
4 <description>Create tabular file for loading into METabolomics EXPlorer database</description> 4 <description>Create tabular file for loading into METabolomics EXPlorer database</description>
5 <command interpreter="python"> 5 <command interpreter="python">
6 export_to_metexp_tabular.py $rankfilter_and_caslookup_combi $msclust_quant_file $output_result 6 export_to_metexp_tabular.py $rankfilter_and_caslookup_combi $msclust_quant_file $output_result
7 $organism $tissue $experiment_name $user_name $column_type 7 $organism $tissue $experiment_name $user_name $column_type
8 </command> 8 </command>
13 help="Select the output file from MsClust (centrotype, mic or sim) which also contain respective spectrum details"/> 13 help="Select the output file from MsClust (centrotype, mic or sim) which also contain respective spectrum details"/>
14 14
15 15
16 <param name="organism" type="text" size="80" 16 <param name="organism" type="text" size="80"
17 label="Organism(s) info" 17 label="Organism(s) info"
18 help="Metadata information to accompany the results when stored in MetExp DB." /> 18 help="Metadata information to accompany the results when stored in MetExp DB." >
19 <validator type="empty_field" message="A value is required."></validator><!-- attribute optional="False" does not seem to work for params so validator is added -->
20 </param>
21
19 <param name="tissue" type="text" size="80" 22 <param name="tissue" type="text" size="80"
20 label="Tissue(s) info" 23 label="Tissue(s) info"
21 help="Metadata information to accompany the results when stored in MetExp DB." /> 24 help="Metadata information to accompany the results when stored in MetExp DB." >
25 <validator type="empty_field" message="A value is required."></validator>
26 </param>
22 27
23 <param name="experiment_name" type="text" size="80" 28 <param name="experiment_name" type="text" size="80"
24 label="Experiment name/code" 29 label="Experiment name/code"
25 help="Name or code to store the results under. This can help you find the results back in MetExpDB." /> 30 help="Name or code to store the results under. This can help you find the results back in MetExpDB." >
31 <validator type="empty_field" message="A value is required."></validator>
32 </param>
26 33
27 <param name="user_name" type="text" size="80" 34 <param name="user_name" type="text" size="80"
28 label="User name" 35 label="User name"
29 help="User name or code to store the results under. This can help you find the results back in MetExpDB." /> 36 help="User name or code to store the results under. This can help you find the results back in MetExpDB." >
37 <validator type="empty_field" message="A value is required."></validator>
38 </param>
30 39
31 <param name="column_type" type="text" size="80" 40 <param name="column_type" type="text" size="80"
32 label="Column type" 41 label="Column type"
33 help="Column type to report with the results. This can help you find the results back in MetExpDB." /> 42 help="Column type to report with the results. This can help you find the results back in MetExpDB." >
43 <validator type="empty_field" message="A value is required."></validator>
44 </param>
34 45
35 </inputs> 46 </inputs>
36 <outputs> 47 <outputs>
37 <data format="tabular" label="${tool.name} on ${on_string}" name="output_result" /> 48 <data format="tabular" label="${tool.name} on ${on_string}" name="output_result" />
38 </outputs> 49 </outputs>