Mercurial > repos > bebatut > humann2

comparison humann2_download_databases.xml @ 0:3d6f37e7e3a8 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty
author bebatut
date Thu, 26 May 2016 10:20:59 -0400
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-1:000000000000 0:3d6f37e7e3a8
1 <tool id="humann2_download_databases" name="Download" version="0.6.1">
2 <description>HUMAnN2 databases</description>
3
4 <macros>
5 <import>humann2_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9 <expand macro="stdio"/>
10
11 <version_command>
12 <![CDATA[
13 humann2_databases --version
14 ]]>
15 </version_command>
16
17 <command><![CDATA[
18 humann2_databases
19 --download $database_selector \${HUMANN2_DIR}/databases
20
21 > $log
22 ]]></command>
23
24 <inputs>
25 <param name="database_selector" type="select" label="Database to download" help="">
26 <option value="chocophlan full">Nucleotide (ChocoPhlAn)</option>
27 <option value="uniref diamond">Protein (UniRef50)</option>
28 </param>
29 </inputs>
30
31 <outputs>
32 <data format="txt" name="log" label="${tool.name}: Log" />
33 </outputs>
34
35 <tests>
36 </tests>
37
38 <help><![CDATA[
39 **What it does**
40
41 HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
42
43 Download HUMAnN2 databases is a tool to download needed nucleotide or protein databases. This tool must be run before using HUMAnN2.
44 ]]></help>
45
46 <expand macro="citations"/>
47 </tool>