Mercurial > repos > matthias > data_manager_dada2

comparison data_manager/dada2_fetcher.xml @ 4:51b90d282704 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 2f47c03d1b775ab796c75c806c1ab247bb51359d
author matthias
date Fri, 10 May 2019 11:52:03 -0400
parents 3a4ee8bf012a
children b899349a9c2b
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3:3a4ee8bf012a 4:51b90d282704
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="dada_fetcher" name="dada2 data manager" version="0.0.5"> 2 <tool id="dada_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.5">
3 <description>Download reference databases</description> 3 <description>Download reference databases</description>
4 <command detect_errors="exit_code"><![CDATA[ 4 <command detect_errors="exit_code"><![CDATA[
5 python '$__tool_directory__/data_manager.py' 5 python '$__tool_directory__/data_manager.py'
6 --out '${out_file}' 6 --out '$out_file'
7 --dataset '$db_cond.db_select'_'$db_cond.version_select' 7 #set dataset = str($db_cond.db_select) + '_' + str($db_cond.version_select)
8 --dataset '$dataset'
8 ]]> 9 ]]>
9 </command> 10 </command>
10 <inputs> 11 <inputs>
11 <conditional name="db_cond"> 12 <conditional name="db_cond">
12 <param name="db_select" type="select" label="Taxonomic database"> 13 <param name="db_select" type="select" label="Taxonomic database">
74 <data name="out_file" format="data_manager_json" /> 75 <data name="out_file" format="data_manager_json" />
75 </outputs> 76 </outputs>
76 <tests> 77 <tests>
77 <test> 78 <test>
78 <param name="db_cond|db_select" value="silva"/> 79 <param name="db_cond|db_select" value="silva"/>
79 <param name="db_cond|db_version" value="132"/> 80 <param name="db_cond|version_select" value="132"/>
80 <output name="out_file" file="silva132_json"/> 81 <output name="out_file" file="silva132_json"/>
81 </test> 82 </test>
82 <test> 83 <test>
83 <param name="db_cond|db_select" value="rdp"/> 84 <param name="db_cond|db_select" value="rdp"/>
84 <param name="db_cond|db_version" value="16"/> 85 <param name="db_cond|version_select" value="16"/>
85 <output name="out_file" file="rdp16_json"/> 86 <output name="out_file" file="rdp16_json"/>
86 </test> 87 </test>
87 <test> 88 <test>
88 <param name="db_cond|db_select" value="greengenes"/> 89 <param name="db_cond|db_select" value="greengenes"/>
89 <param name="db_cond|db_version" value="13.84"/> 90 <param name="db_cond|version_select" value="13.84"/>
90 <output name="out_file" file="greengenes13.84_json"/> 91 <output name="out_file" file="greengenes13.84_json"/>
91 </test> 92 </test>
92 <test> 93 <test>
93 <param name="db_cond|db_select" value="unite"/> 94 <param name="db_cond|db_select" value="unite"/>
94 <param name="db_cond|db_version" value="8.0_fungi"/> 95 <param name="db_cond|version_select" value="8.0_fungi"/>
95 <output name="out_file" file="unite8fungi_json"/> 96 <output name="out_file" file="unite8fungi_json"/>
96 </test> 97 </test>
97 <test> 98 <test>
98 <param name="db_cond|db_select" value="RefSeq_RDP"/> 99 <param name="db_cond|db_select" value="RefSeq_RDP"/>
99 <param name="db_cond|db_version" value="2018_05"/> 100 <param name="db_cond|version_select" value="2018_05"/>
100 <output name="out_file" file="RefSeq_RDP2018_json"/> 101 <output name="out_file" file="RefSeq_RDP2018_json"/>
101 </test> 102 </test>
102 <test> 103 <test>
103 <param name="db_cond|db_select" value="gtdb"/> 104 <param name="db_cond|db_select" value="gtdb"/>
104 <param name="db_cond|db_version" value="2018_11"/> 105 <param name="db_cond|version_select" value="2018_11"/>
105 <output name="out_file" file="gtdb2018_json"/> 106 <output name="out_file" file="gtdb2018_json"/>
106 </test> 107 </test>
107 <test> 108 <test>
108 <param name="db_cond|db_select" value="hitdb"/> 109 <param name="db_cond|db_select" value="hitdb"/>
109 <param name="db_cond|db_version" value="1"/> 110 <param name="db_cond|version_select" value="1"/>
110 <output name="out_file" file="hitdb1_json"/> 111 <output name="out_file" file="hitdb1_json"/>
111 </test> 112 </test>
112 <test> 113 <test>
113 <param name="db_cond|db_select" value="silva_euk_18S"/> 114 <param name="db_cond|db_select" value="silva_euk_18S"/>
114 <param name="db_cond|db_version" value="132"/> 115 <param name="db_cond|version_select" value="132"/>
115 <output name="out_file" file="silvaeuk132_json"/> 116 <output name="out_file" file="silvaeuk132_json"/>
116 </test> 117 </test>
117 <test> 118 <test>
118 <param name="db_cond|db_select" value="PR2"/> 119 <param name="db_cond|db_select" value="PR2"/>
119 <param name="db_cond|db_version" value="4.11.1"/> 120 <param name="db_cond|version_select" value="4.11.1"/>
120 <output name="out_file" file="PR24.11.1_json"/> 121 <output name="out_file" file="PR24.11.1_json"/>
121 </test> 122 </test>
122 </tests> 123 </tests>
123 <help><![CDATA[ 124 <help><![CDATA[
124 Public Reference databases maintained by the DADA2 project 125 Public Reference databases maintained by the DADA2 project