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annotate 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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d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="2.5.0">
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3 <description>output for Krona</description>
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5 <macros>
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6 <import>metaphlan2_macros.xml</import>
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7 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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12 <version_command>
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13 <![CDATA[
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14 metaphlan2krona.py -v
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15 ]]>
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16 </version_command>
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18 <command>
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19 <![CDATA[
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20 metaphlan2krona.py
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21 -p $input_file
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22 -k $krona
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23 ]]>
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24 </command>
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26 <inputs>
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27 <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/>
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28 </inputs>
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30 <outputs>
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31 <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Krona file" />
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32 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input_file" value="community_profile.tabular"/>
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37 <output name="krona" file="formatted_to_krona.tabular"/>
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38 </test>
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39 </tests>
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41 <help><![CDATA[
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43 **What it does**
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44
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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/>`_.
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47 This tool format MetaPhlAn2 output for Krona.
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49 ]]></help>
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51 <citations>
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52 <citation type="doi">10.1038/nmeth.3589</citation>
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53 </citations>
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54 </tool>