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comparison metaphlan2krona.xml @ 1:8991e05c44e4 draft default tip

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
author bebatut
date Thu, 16 Jun 2016 06:08:11 -0400
parents d2448d2bf1f8
children
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0:d2448d2bf1f8 1:8991e05c44e4
5 <macros> 5 <macros>
6 <import>metaphlan2_macros.xml</import> 6 <import>metaphlan2_macros.xml</import>
7 </macros> 7 </macros>
8 8
9 <expand macro="requirements"/> 9 <expand macro="requirements"/>
10 <expand macro="stdio"/> 10 <expand macro="stdio"/>
11 11
12 <version_command> 12 <version_command>
13 <![CDATA[ 13 <![CDATA[
14 metaphlan2krona.py -v 14 metaphlan2krona.py -v
15 ]]> 15 ]]>
16 </version_command> 16 </version_command>
17 17
18 <command> 18 <command>
19 <![CDATA[ 19 <![CDATA[
20 metaphlan2krona.py 20 metaphlan2krona.py
21 -p $input_file 21 -p $input_file
22 -k $krona 22 -k $krona
23 ]]> 23 ]]>
24 </command> 24 </command>
26 <inputs> 26 <inputs>
27 <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/> 27 <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/>
28 </inputs> 28 </inputs>
29 29
30 <outputs> 30 <outputs>
31 <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Krona file" /> 31 <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" />
32 </outputs> 32 </outputs>
33 33
34 <tests> 34 <tests>
35 <test> 35 <test>
36 <param name="input_file" value="community_profile.tabular"/> 36 <param name="input_file" value="community_profile.tabular"/>
37 <output name="krona" file="formatted_to_krona.tabular"/> 37 <output name="krona" file="formatted_to_krona.tabular"/>
38 </test> 38 </test>
39 </tests> 39 </tests>
40 40
41 <help><![CDATA[ 41 <help><![CDATA[
42 42
43 **What it does** 43 **What it does**
44 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/>`_. 45 MetaPhlAn is a computational tool to profile the structure and 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 46
47 This tool format MetaPhlAn2 output for Krona. 47 This tool formats MetaPhlAn2 output to be ready for Krona.
48 48
49 ]]></help> 49 ]]></help>
50 50
51 <citations> 51 <citations>
52 <citation type="doi">10.1038/nmeth.3589</citation> 52 <citation type="doi">10.1038/nmeth.3589</citation>