Mercurial > repos > iuc > data_manager_pharokka
comparison data_manager/pharokka_db_fetcher.xml @ 1:50caca83e7c9 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
author | iuc |
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date | Sun, 06 Aug 2023 10:11:42 +0000 |
parents | 97f310b8e308 |
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0:97f310b8e308 | 1:50caca83e7c9 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="pharokka_db_fetcher" name="phrokka DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | 2 <tool id="pharokka_db_fetcher" name="phrokka DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
3 <description>Fetches the DB required for phrokka</description> | |
3 <macros> | 4 <macros> |
4 <import>macros.xml</import> | 5 <import>macros.xml</import> |
5 </macros> | 6 </macros> |
6 <expand macro="biotools" /> | 7 <expand macro="biotools" /> |
7 <expand macro="requirements" /> | 8 <expand macro="requirements" /> |
8 <expand macro="version" /> | 9 <expand macro="version" /> |
9 <description>Fetches the DB required for phrokka</description> | 10 |
10 <command detect_errors="exit_code"> | 11 <command detect_errors="exit_code"> |
11 <![CDATA[ | 12 <![CDATA[ |
12 python '$__tool_directory__/data_manager_fetch_pharokka_db.py' --out '${out_file}' --version '${version}' | 13 python '$__tool_directory__/data_manager_fetch_pharokka_db.py' --out '${out_file}' --version '${version}' |
13 $test_data_manager | 14 $test_data_manager |
14 ]]> | 15 ]]> |
15 </command> | 16 </command> |
16 <inputs> | 17 <inputs> |
17 <param name="test_data_manager" type="hidden" value=""/> | 18 <param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Copy minimal test DB and create mock data table entry." /> |
18 <param argument="--version" type="text" value="v1.2.0" help="Check https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102 for current version."/> | 19 |
20 <!-- <param name="test_data_manager" type="text" value=""/> --> | |
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."/> | |
19 </inputs> | 22 </inputs> |
20 <outputs> | 23 <outputs> |
21 <data format="data_manager_json" name="out_file" /> | 24 <data format="data_manager_json" name="out_file" /> |
22 </outputs> | 25 </outputs> |
23 <tests> | 26 <tests> |
33 </assert_contents> | 36 </assert_contents> |
34 </output> | 37 </output> |
35 </test> | 38 </test> |
36 </tests> | 39 </tests> |
37 <help> | 40 <help> |
41 <![CDATA[ | |
42 Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. | |
43 This data manager fetches the DB using the build-in tool download script. | |
44 The version must be checked here: https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102 | |
45 ]]> | |
38 </help> | 46 </help> |
39 <expand macro="citations" /> | 47 <expand macro="citations" /> |
40 <expand macro="creator" /> | 48 <expand macro="creator" /> |
41 </tool> | 49 </tool> |