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comparison influx_data_manager.xml @ 0:6daf2eaa1509 draft

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planemo upload for repository https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager commit 6e361ee7b6e2ebc70e1c3033b88e316d0854ff6b
author workflow4metabolomics
date Fri, 09 Feb 2024 08:19:16 +0000
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children c722e4bdeb37
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-1:000000000000 0:6daf2eaa1509
1 <tool id="influx_data_manager" name="Influx Data Connector: Handling influx_si data inputs in Galaxy workflows" version="@TOOL_VERSION@+galaxy0" profile="23.0">
2 <macros>
3 <token name='@TOOL_VERSION@'>1.0.0</token>
4 </macros>
5 <requirements>
6 <requirement type='package' version='@TOOL_VERSION@'>influx-si-data-manager</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 influx_data_manager
10 --physiofit '$physiofit'
11 --isocor '$isocor'
12 --linp '$linp'
13 --netw '$netw'
14 --mmet '$mmet'
15 --cnstr '$cnstr'
16 --tvar '$tvar'
17 --opt '$opt'
18 --log '$stdout'
19 $verbose
20 2> '$stderr' && cat '$stdout'
21 ]]></command>
22 <inputs>
23 <param type='data' format='tabular,txt' argument='--netw' label='File containing network for experiments (.netw file)' optional='false'/>
24 <param type='data' format='tabular,txt' argument='--isocor' label='Output of isocor which corresponds to the .miso input (.tsv file)' optional='false'/>
25 <param type='data' format='tabular,txt' argument='--tvar' label='File containing types of variables for experiments (.tvar file)' optional='false'/>
26 <param type='data' format='tabular,txt' argument='--physiofit' label='Output of physiofit which corresponds to the .mflux input (.csv file)' optional='true'/>
27 <param type='data' format='tabular,txt' argument='--linp' label='File contianing label inputs for experiments (.linp file)' optional='true'/>
28 <param type='data' format='tabular,txt' argument='--mmet' label='File containing specie concentrations for experiments (.mmet file)' optional='true'/>
29 <param type='data' format='tabular,txt' argument='--cnstr' label='File containing constraints onf fluxes and specie concentrations for experiments (.constr file)' optional='true'/>
30 <param type='data' format='tabular,txt' argument='--opt' label='File containing options for influx_si (.opt file)' optional='true'/>
31 <param name='verbose' type='boolean' truevalue='--verbose' falsevalue='' label='Debug mode' help='Select "Yes" to have debug logs be printed out'/>
32 </inputs>
33 <outputs>
34 <data format='txt' name='stdout' label='Run log'/>
35 <collection type='list' label='Influx_si input files' name='list_output'>
36 <discover_datasets pattern='__name_and_ext__' format='zip'/>
37 </collection>
38 <data format='txt' name='stderr' label='Influx DM error log'/>
39 </outputs>
40 <tests>
41 <test expect_num_outputs='3'>
42 <param name='netw' value='galaxy_test.netw'/>
43 <param name='isocor' value='galaxy_test.tsv'/>
44 <param name='tvar' value='galaxy_test.tvar'/>
45 <param name='physiofit' value='galaxy_test.csv'/>
46 <param name='linp' value='galaxy_test.linp'/>
47 <!-- <param name='in_mmet' value='galaxy_test.mmet'/> FOR FUTURE USE IN INSTATIONARY SETTING -->
48 <param name='cnstr' value='galaxy_test.cnstr'/>
49 <param name='opt' value='galaxy_test.opt'/>
50 <param name='verbose' value='true'/>
51 <output_collection name='list_output' type='list'>
52 <element name='Sample_1'>
53 <assert_contents>
54 <has_archive_member path='Sample_1.miso'>
55 <has_text_matching expression='sample\tId\tComment\tSpecie\tFragment\tDataset\tIsospecies\tSD\tTime'/>
56 <has_n_lines n='30'/>
57 </has_archive_member>
58 <has_archive_member path='Sample_1.mflux'>
59 <has_text_matching expression='Id\tComment\tFlux\tValue\tSD'/>
60 <has_text_matching expression='Glc_q'/>
61 <has_n_lines n='4'/>
62 </has_archive_member>
63 <has_archive_member path='Sample_1.netw'>
64 <has_n_lines n='87'/>
65 </has_archive_member>
66 <has_archive_member path='Sample_1.tvar'/>
67 <has_archive_member path='Sample_1.linp'/>
68 <has_archive_member path='Sample_1.cnstr'/>
69 <has_archive_member path='Sample_1.opt'/>
70 </assert_contents>
71 </element>
72 </output_collection>
73 </test>
74 </tests>
75 <help><![CDATA[
76 This tool is meant to handle the input files for influx_si within workflows. It is not meant to be used as a stand-alone within the platform.
77 ]]></help>
78 <citations>
79 <citation type='bibtex'>
80 @misc{
81 githubinflux_si,
82 author = {Le Gregam, Loic},
83 year = {2024},
84 title = {Influx-si-data-manager},
85 }
86 </citation>
87 </citations>
88 </tool>