Mercurial > repos > iuc > data_manager_humann2_database_downloader
view data_manager/data_manager_humann2_download.xml @ 3:854d9862a9f1 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author | iuc |
---|---|
date | Tue, 01 Aug 2017 07:54:30 -0400 |
parents | 6112a571f012 |
children |
line wrap: on
line source
<tool id="data_manager_humann2_download" name="HUMAnN2 download" version="@VERSION@.0" tool_type="manage_data"> <description>Download HUMAnN2 database</description> <macros> <token name="@VERSION@">0.11.1</token> </macros> <requirements> <requirement type="package" version="@VERSION@">humann2</requirement> </requirements> <stdio> <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> <exit_code range="1:" level="fatal" description="Error" /> </stdio> <command> python '$__tool_directory__/data_manager_humann2_download.py' --database '$db.database' --build $db.build '${out_file}' </command> <inputs> <conditional name="db"> <param name="database" type="select" label="Type of database to download"> <option value="chocophlan" selected="true">Nucleotide database</option> <option value="uniref">Protein database</option> </param> <when value="chocophlan"> <param name="build" type="select" label="Build for nucleotide database"> <option value="full" selected="true">Full</option> <option value="DEMO">Demo</option> </param> </when> <when value="uniref"> <param name="build" type="select" label="Build for protein database"> <option value="uniref50_diamond">Full UniRef50</option> <option value="uniref50_ec_filtered_diamond">EC-filtered UniRef50</option> <option value="uniref50_GO_filtered_rapsearch2">GO filtered UniRef50 for rapsearch2</option> <option value="uniref90_diamond" selected="true">Full UniRef90</option> <option value="uniref90_ec_filtered_diamond">EC-filtered UniRef90</option> <option value="DEMO_diamond">Demo</option> </param> </when> </conditional> </inputs> <outputs> <data name="out_file" format="data_manager_json" label="${tool.name}" /> </outputs> <tests> </tests> <help> This tool downloads the HUMAnN2 databases. Read more about the tool at http://huttenhower.sph.harvard.edu/humann2/manual . </help> <citations> <citation type="doi">10.1371/journal.pcbi.1003153</citation> </citations> </tool>