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comparison data_manager/pharokka_db_fetcher.xml @ 1:bba8135dc024 draft default tip

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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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0:3b3daabcc63e 1:bba8135dc024
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>