Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy

comparison data_manager/ncbi_taxonomy_fetcher.xml @ 3:bdd8632fa9fb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
author iuc
date Mon, 06 Jul 2020 19:32:35 -0400
parents 4af4e175db0d
children d6acd5cd497b
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2:4af4e175db0d 3:bdd8632fa9fb
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.1"> 2 <tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.2">
3 <description>taxonomy downloader</description> 3 <description>taxonomy downloader</description>
4 <requirements>
5 <requirement type="package" version="3.7">python</requirement>
6 </requirements>
4 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
5 <![CDATA[ 8 <![CDATA[
6 python '$__tool_directory__/data_manager.py' --out '${out_file}' 9 python '$__tool_directory__/data_manager.py' --out '${out_file}'
7 #if $taxonomy_url: 10 #if $taxonomy_url:
8 --url '${taxonomy_url}' 11 --url '${taxonomy_url}'
17 <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" /> 20 <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" />
18 </inputs> 21 </inputs>
19 <outputs> 22 <outputs>
20 <data name="out_file" format="data_manager_json" /> 23 <data name="out_file" format="data_manager_json" />
21 </outputs> 24 </outputs>
25 <tests>
26 <test>
27 <param name="database_name" value="tax_name"/>
28 <param name="database_id" value="tax_id"/>
29 <output name="out_file" value="taxonomy.json"/>
30 </test>
31 </tests>
32 <help>
33 Download a taxonomy dump from a provided URL.
34 The default URL is the latest dump from NCBI taxonomy.
35 </help>
22 </tool> 36 </tool>