Mercurial > repos > iuc > data_manager_cat

comparison data_manager/data_manager_cat.xml @ 0:cffd8e2382cf draft

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"planemo upload commit 4e5a8d7629d90c41219b48b648dd4ab675b84af0"
author iuc
date Mon, 09 Dec 2019 10:28:15 -0500
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children 472dabcb03bf
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1 <tool id="data_manager_cat" name="CAT DB" version="5.0.3.0" tool_type="manage_data" profile="18.09">
2 <description>Install a new CAT database</description>
3 <requirements>
4 <requirement type="package" version="5.0.3">cat</requirement>
5 </requirements>
6 <version_command><![CDATA[ CAT --version ]]></version_command>
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p '$out_file.extra_files_path' &&
9 python '${__tool_directory__}/data_manager_cat.py'
10 --config_file '$out_file'
11 --install_path '$out_file.extra_files_path'
12 #if $db.src == 'download'
13 --db_url '$db.db_url'
14 #end if
15 ]]></command>
16 <inputs>
17 <conditional name="db">
18 <param name="src" type="select" label="Download or Build DBs">
19 <option value="download">download</option>
20 <option value="build">build</option>
21 </param>
22 <when value="download">
23 <param name="db_url" type="text" label="DB URL at https://tbb.bio.uu.nl/bastiaan/CAT_prepare/"
24 help="example: https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190719.tar.gz">
25 </param>
26 </when>
27 <when value="build">
28 </when>
29 </conditional>
30 </inputs>
31 <outputs>
32 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
33 </outputs>
34 <tests>
35 <test>
36 <conditional name="db">
37 <param name="src" value="download"/>
38 <param name="db_url" value="https://github.com/galaxyproject/tools-iuc/blob/ce82f787f1f035debfc86de09a271a9ec8d27e0e/data_managers/data_manager_cat/test-data/CAT_prepare_test.tar.gz?raw=true"/>
39 </conditional>
40 <output name="out_file">
41 <assert_contents>
42 <has_text text="CAT_prepare_test/taxonomy" />
43 </assert_contents>
44 </output>
45 </test>
46 </tests>
47 <help><![CDATA[
48 This tool prepares reference data for CAT, the Contig Annotation Tool.
49 It can either download prebuilt reference data from https://tbb.bio.uu.nl/bastiaan/CAT_prepare/
50 or build new reference data using the CAT prepare application.
51
52 This requires at least 100GB of RAM, 250GB of disk space, and 24 hours.
53 ]]></help>
54 <expand macro="citations" />
55 </tool>