Mercurial > repos > iuc > data_manager_cat
comparison data_manager/data_manager_cat.xml @ 0:cffd8e2382cf draft
"planemo upload commit 4e5a8d7629d90c41219b48b648dd4ab675b84af0"
author | iuc |
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date | Mon, 09 Dec 2019 10:28:15 -0500 |
parents | |
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> |