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comparison metaphlan2krona.xml @ 0:d2448d2bf1f8 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
author bebatut
date Wed, 01 Jun 2016 10:45:26 -0400
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children 8991e05c44e4
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-1:000000000000 0:d2448d2bf1f8
1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="2.5.0">
2
3 <description>output for Krona</description>
4
5 <macros>
6 <import>metaphlan2_macros.xml</import>
7 </macros>
8
9 <expand macro="requirements"/>
10 <expand macro="stdio"/>
11
12 <version_command>
13 <![CDATA[
14 metaphlan2krona.py -v
15 ]]>
16 </version_command>
17
18 <command>
19 <![CDATA[
20 metaphlan2krona.py
21 -p $input_file
22 -k $krona
23 ]]>
24 </command>
25
26 <inputs>
27 <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/>
28 </inputs>
29
30 <outputs>
31 <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Krona file" />
32 </outputs>
33
34 <tests>
35 <test>
36 <param name="input_file" value="community_profile.tabular"/>
37 <output name="krona" file="formatted_to_krona.tabular"/>
38 </test>
39 </tests>
40
41 <help><![CDATA[
42
43 **What it does**
44
45 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
46
47 This tool format MetaPhlAn2 output for Krona.
48
49 ]]></help>
50
51 <citations>
52 <citation type="doi">10.1038/nmeth.3589</citation>
53 </citations>
54 </tool>