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comparison export_to_metexp_tabular.xml @ 0:dffc38727496

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author pieter.lukasse@wur.nl
date Sat, 07 Feb 2015 22:02:00 +0100
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1 <tool id="export_to_metexp_tabular"
2 name="METEXP - Tabular file"
3 version="0.2.0">
4 <description>Create tabular file for loading into METabolomics EXPlorer database</description>
5 <command interpreter="python">
6 export_to_metexp_tabular.py
7 $rankfilter_and_caslookup_combi
8 $msclust_quant_file
9 $output_result
10 "$organism"
11 "$tissue"
12 "$experiment_name"
13 "$user_name"
14 "$column_type"
15 </command>
16 <inputs>
17 <param format="tabular" name="rankfilter_and_caslookup_combi" type="data" label="RIQC-Combine RankFilter and CasLookup output"
18 help="Select the (multi) output file from the 'Combine RankFilter and CasLookup' tool"/>
19 <param format="tabular" name="msclust_quant_file" type="data" label="MusClust-quantification file output"
20 help="Select the output file from MsClust (centrotype, mic or sim) which also contain respective spectrum details"/>
21
22
23 <param name="organism" type="text" size="80"
24 label="Organism(s) info"
25 help="Metadata information to accompany the results when stored in MetExp DB." >
26 <validator type="empty_field" message="A value is required."></validator><!-- attribute optional="False" does not seem to work for params so validator is added -->
27 </param>
28
29 <param name="tissue" type="text" size="80"
30 label="Tissue(s) info"
31 help="Metadata information to accompany the results when stored in MetExp DB." >
32 <validator type="empty_field" message="A value is required."></validator>
33 </param>
34
35 <param name="experiment_name" type="text" size="80"
36 label="Experiment name/code"
37 help="Name or code to store the results under. This can help you find the results back in MetExpDB." >
38 <validator type="empty_field" message="A value is required."></validator>
39 </param>
40
41 <param name="user_name" type="text" size="80"
42 label="User name"
43 help="User name or code to store the results under. This can help you find the results back in MetExpDB." >
44 <validator type="empty_field" message="A value is required."></validator>
45 </param>
46
47 <param name="column_type" type="text" size="80"
48 label="Column type"
49 help="Column type to report with the results. This can help you find the results back in MetExpDB." >
50 <validator type="empty_field" message="A value is required."></validator>
51 </param>
52
53 </inputs>
54 <outputs>
55 <data format="tabular" label="${tool.name} on ${on_string}" name="output_result" />
56 </outputs>
57 <help>
58 .. class:: infomark
59
60 Tool to combine output from the tools RankFilter, CasLookup and MsClust
61 into a tabular file that can be uploaded to the METabolomics EXPlorer (MetExp) database.
62
63 RankFilter, CasLookup are already combined by 'RIQC-Combine RankFilter and CasLookup' tool so here we will use
64 this result.
65
66 **Notes**
67
68 Extra calculations performed:
69 - The columns MM and MW are also added here and are derived from the column FORMULA found in RankFilter, CasLookup combined result.
70
71 So in total here we merge 2 files and calculate one new column.
72
73
74 </help>
75 </tool>