Mercurial > repos > workflow4metabolomics > influx_si_data_manager

annotate 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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6daf2eaa1509 planemo upload for repository https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager commit 6e361ee7b6e2ebc70e1c3033b88e316d0854ff6b
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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">
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2 <macros>
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3 <token name='@TOOL_VERSION@'>1.0.0</token>
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4 </macros>
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5 <requirements>
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6 <requirement type='package' version='@TOOL_VERSION@'>influx-si-data-manager</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 influx_data_manager
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10 --physiofit '$physiofit'
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11 --isocor '$isocor'
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12 --linp '$linp'
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13 --netw '$netw'
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14 --mmet '$mmet'
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15 --cnstr '$cnstr'
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16 --tvar '$tvar'
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17 --opt '$opt'
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18 --log '$stdout'
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19 $verbose
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20 2> '$stderr' && cat '$stdout'
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21 ]]></command>
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22 <inputs>
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23 <param type='data' format='tabular,txt' argument='--netw' label='File containing network for experiments (.netw file)' optional='false'/>
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24 <param type='data' format='tabular,txt' argument='--isocor' label='Output of isocor which corresponds to the .miso input (.tsv file)' optional='false'/>
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25 <param type='data' format='tabular,txt' argument='--tvar' label='File containing types of variables for experiments (.tvar file)' optional='false'/>
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26 <param type='data' format='tabular,txt' argument='--physiofit' label='Output of physiofit which corresponds to the .mflux input (.csv file)' optional='true'/>
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27 <param type='data' format='tabular,txt' argument='--linp' label='File contianing label inputs for experiments (.linp file)' optional='true'/>
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28 <param type='data' format='tabular,txt' argument='--mmet' label='File containing specie concentrations for experiments (.mmet file)' optional='true'/>
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29 <param type='data' format='tabular,txt' argument='--cnstr' label='File containing constraints onf fluxes and specie concentrations for experiments (.constr file)' optional='true'/>
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30 <param type='data' format='tabular,txt' argument='--opt' label='File containing options for influx_si (.opt file)' optional='true'/>
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31 <param name='verbose' type='boolean' truevalue='--verbose' falsevalue='' label='Debug mode' help='Select "Yes" to have debug logs be printed out'/>
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32 </inputs>
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33 <outputs>
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34 <data format='txt' name='stdout' label='Run log'/>
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35 <collection type='list' label='Influx_si input files' name='list_output'>
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36 <discover_datasets pattern='__name_and_ext__' format='zip'/>
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37 </collection>
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38 <data format='txt' name='stderr' label='Influx DM error log'/>
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39 </outputs>
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40 <tests>
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41 <test expect_num_outputs='3'>
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42 <param name='netw' value='galaxy_test.netw'/>
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43 <param name='isocor' value='galaxy_test.tsv'/>
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44 <param name='tvar' value='galaxy_test.tvar'/>
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45 <param name='physiofit' value='galaxy_test.csv'/>
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46 <param name='linp' value='galaxy_test.linp'/>
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47 <!-- <param name='in_mmet' value='galaxy_test.mmet'/> FOR FUTURE USE IN INSTATIONARY SETTING -->
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48 <param name='cnstr' value='galaxy_test.cnstr'/>
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49 <param name='opt' value='galaxy_test.opt'/>
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50 <param name='verbose' value='true'/>
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51 <output_collection name='list_output' type='list'>
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52 <element name='Sample_1'>
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53 <assert_contents>
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54 <has_archive_member path='Sample_1.miso'>
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55 <has_text_matching expression='sample\tId\tComment\tSpecie\tFragment\tDataset\tIsospecies\tSD\tTime'/>
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56 <has_n_lines n='30'/>
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57 </has_archive_member>
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58 <has_archive_member path='Sample_1.mflux'>
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59 <has_text_matching expression='Id\tComment\tFlux\tValue\tSD'/>
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60 <has_text_matching expression='Glc_q'/>
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61 <has_n_lines n='4'/>
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62 </has_archive_member>
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63 <has_archive_member path='Sample_1.netw'>
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64 <has_n_lines n='87'/>
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65 </has_archive_member>
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66 <has_archive_member path='Sample_1.tvar'/>
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67 <has_archive_member path='Sample_1.linp'/>
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68 <has_archive_member path='Sample_1.cnstr'/>
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69 <has_archive_member path='Sample_1.opt'/>
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70 </assert_contents>
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71 </element>
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72 </output_collection>
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73 </test>
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74 </tests>
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75 <help><![CDATA[
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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.
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77 ]]></help>
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78 <citations>
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79 <citation type='bibtex'>
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80 @misc{
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81 githubinflux_si,
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82 author = {Le Gregam, Loic},
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83 year = {2024},
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84 title = {Influx-si-data-manager},
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85 }
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86 </citation>
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87 </citations>
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88 </tool>