Mercurial > repos > iuc > data_manager_pharokka

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
author iuc
date Sun, 06 Aug 2023 10:10:51 +0000
parents 3b3daabcc63e
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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1 <?xml version="1.0"?>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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2 <tool id="pharokka_db_fetcher" name="phrokka DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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3 <description>Fetches the DB required for phrokka</description>
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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4 <macros>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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5 <import>macros.xml</import>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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6 </macros>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
iuc
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7 <expand macro="biotools" />
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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8 <expand macro="requirements" />
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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9 <expand macro="version" />
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bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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10
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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11 <command detect_errors="exit_code">
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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12 <![CDATA[
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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13 python '$__tool_directory__/data_manager_fetch_pharokka_db.py' --out '${out_file}' --version '${version}'
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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14 $test_data_manager
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15 ]]>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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16 </command>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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17 <inputs>
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bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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18 <param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Copy minimal test DB and create mock data table entry." />
bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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20 <!-- <param name="test_data_manager" type="text" value=""/> -->
bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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21 <param argument="--version" type="text" value="1.2.0" help="Check https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102 for current version. The default value is recommended."/>
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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22 </inputs>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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23 <outputs>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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24 <data format="data_manager_json" name="out_file" />
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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25 </outputs>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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26 <tests>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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27 <test expect_num_outputs="1">
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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28 <param name="test_data_manager" value="--test"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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29 <param name="version" value="v1.2.0"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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30 <output name="out_file">
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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31 <assert_contents>
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32 <has_text text="Pharokka DB version"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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33 <has_text text="db_from_"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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34 <has_text text="pharokka_db"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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35 <has_text text="v1.2.0"/>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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36 </assert_contents>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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37 </output>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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38 </test>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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39 </tests>
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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40 <help>
1
bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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41 <![CDATA[
bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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42 Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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43 This data manager fetches the DB using the build-in tool download script.
bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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44 The version must be checked here: https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102
bba8135dc024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
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45 ]]>
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3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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46 </help>
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47 <expand macro="citations" />
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48 <expand macro="creator" />
3b3daabcc63e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13
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49 </tool>