Mercurial > repos > sanbi-uwc > data_manager_fetch_artic_primers
annotate data_manager/fetch_artic_primers.xml @ 3:6114f017f819 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
author | sanbi-uwc |
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date | Fri, 17 Apr 2020 11:42:59 +0000 |
parents | 119f459fc35f |
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3
6114f017f819
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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1 <tool id="fetch_artic_primers" name="ARTIC primer data manager" version="0.0.4" tool_type="manage_data" profile="19.05"> |
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c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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2 <requirements> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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3 <requirement type="package">python</requirement> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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4 <requirement type="package" version="2.22.0">requests</requirement> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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5 </requirements> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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6 <!-- fetch all the primers in one go --> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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7 <command detect_errors="exit_code"> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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8 python '$__tool_directory__/fetch_artic_primers.py' |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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9 --galaxy_datamanager_filename '${output_file}' |
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59b3556d9ec8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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10 --primers '${primers}' |
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c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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11 </command> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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12 <inputs> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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13 <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch"> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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14 <option value="ARTICv1" selected="true">ARTIC v1</option> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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15 <option value="ARTICv2" selected="true">ARTIC v2</option> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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16 <option value="ARTICv3" selected="true">ARTIC v3</option> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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17 </param> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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18 </inputs> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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19 <outputs> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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20 <data name="output_file" format="data_manager_json"/> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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21 </outputs> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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22 <tests> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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23 <test> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
parents:
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24 <param name="primers" value="ARTICv1,ARTICv2,ARTICv3"/> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
parents:
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25 <output name="output_file"> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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26 <assert_contents> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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27 <has_text text="ARTIC"/> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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28 </assert_contents> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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29 </output> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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30 </test> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
parents:
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31 </tests> |
c401f63b3d12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"
sanbi-uwc
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32 </tool> |