Mercurial > repos > iuc > data_manager_humann2_database_downloader
comparison data_manager/data_manager_humann2_download.xml @ 0:048593e41359 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
author | iuc |
---|---|
date | Sun, 12 Mar 2017 14:33:34 -0400 |
parents | |
children | 1316375a8cbb |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:048593e41359 |
---|---|
1 <tool id="data_manager_humann2_download" name="HUMAnN2 download" version="0.9.9" tool_type="manage_data"> | |
2 <description>Download HUMAnN2 database</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.9.9">humann2</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
8 <exit_code range="1:" level="fatal" description="Error" /> | |
9 </stdio> | |
10 <command interpreter="python"> | |
11 data_manager_humann2_download.py | |
12 --database '$db.database' | |
13 --build '$db.build' | |
14 '${out_file}' | |
15 </command> | |
16 <inputs> | |
17 <conditional name="db"> | |
18 <param name="database" type="select" label="Type of database to download"> | |
19 <option value="chocophlan" selected="true">Nucleotide database</option> | |
20 <option value="uniref">Protein database</option> | |
21 </param> | |
22 <when value="chocophlan"> | |
23 <param name="build" type="select" label="Build for nucleotide database"> | |
24 <option value="full" selected="true">Full</option> | |
25 <option value="DEMO">Demo</option> | |
26 </param> | |
27 </when> | |
28 <when value="uniref"> | |
29 <param name="build" type="select" label="Build for protein database"> | |
30 <option value="uniref50_diamond">Full UniRef50</option> | |
31 <option value="uniref50_ec_filtered_diamond">EC-filtered UniRef50</option> | |
32 <option value="uniref50_GO_filtered_rapsearch2">GO filtered UniRef50 for rapsearch2</option> | |
33 <option value="uniref90_diamond" selected="true">Full UniRef50</option> | |
34 <option value="uniref90_ec_filtered_diamond">EC-filtered UniRef90</option> | |
35 <option value="DEMO_diamond">Demo</option> | |
36 </param> | |
37 </when> | |
38 </conditional> | |
39 </inputs> | |
40 <outputs> | |
41 <data name="out_file" format="data_manager_json" label="${tool.name}"/> | |
42 </outputs> | |
43 <tests> | |
44 </tests> | |
45 <help> | |
46 | |
47 This tool downloads the HUMAnN2 databases. | |
48 | |
49 `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_. | |
50 | |
51 </help> | |
52 <citations> | |
53 <citation type="doi">10.1371/journal.pcbi.1003153</citation> | |
54 <yield /> | |
55 </citations> | |
56 </tool> |