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comparison data_manager/data_manager_cat.xml @ 0:f59e7e242bde draft

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planemo upload commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
author jjohnson
date Sun, 24 Nov 2019 21:54:57 -0500
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1 <tool id="data_manager_cat" name="CAT DB" version="@VERSION@.0" tool_type="manage_data">
2 <description>Install a new CAT database</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[
9 #import json, os
10 #set params = json.loads(open(str($out_file)).read())
11 #set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
12 mkdir -p $install_path &&
13 python '${__tool_directory__}/data_manager_cat.py' --config_file '$out_file' --install_path '$install_path'
14 #if $db.src == 'download'
15 --db_url '$db_url'
16 #end if
17 ]]></command>
18 <inputs>
19 <conditional name="db">
20 <param name="src" type="select" label="Download or Build DBs">
21 <option value="download">download</option>
22 <option value="build">build</option>
23 </param>
24 <when value="download">
25 <param name="db_url" type="text" label="DB rul at https://tbb.bio.uu.nl/bastiaan/CAT_prepare/"
26 help="example: https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190719.tar.gz">
27 </param>
28 </when>
29 <when value="build">
30 </when>
31 </conditional>
32 </inputs>
33 <outputs>
34 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
35 </outputs>
36 <tests>
37 </tests>
38 <help><![CDATA[
39 This tool prepares reference data for CAT, the Contig Annotation Tool.
40 It can either download prebuilt reference data from https://tbb.bio.uu.nl/bastiaan/CAT_prepare/
41 or build new reference data using the CAT prepare application.
42 ]]></help>
43 <expand macro="citations" />
44 </tool>