Mercurial > repos > iuc > metaphlan2krona

annotate metaphlan2krona.xml @ 1:0ff3f7810262 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
author iuc
date Fri, 19 Mar 2021 09:38:23 +0000
parents fdbd63e92b01
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="@WRAPPER_VERSION@.0">
fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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3 <description>output for Krona</description>
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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5 <macros>
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6 <import>metaphlan2_macros.xml</import>
fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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7 </macros>
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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12 <version_command>metaphlan2krona.py -v</version_command>
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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14 <command>
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15 <![CDATA[
fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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16 metaphlan2krona.py
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17 --profile '$profile'
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18 -k '$krona'
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19 ]]>
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20 </command>
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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22 <inputs>
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23 <param argument="--profile" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)"/>
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24 </inputs>
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26 <outputs>
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27 <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" />
fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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28 </outputs>
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30 <tests>
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31 <test>
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32 <param name="profile" value="community_profile.tabular"/>
fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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33 <output name="krona" file="formatted_to_krona.tabular"/>
fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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34 </test>
fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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35 </tests>
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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37 <help><![CDATA[
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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39 **What it does**
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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41 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/>`_.
fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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43 This tool formats MetaPhlAn2 output to be ready for Krona.
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45 ]]></help>
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fdbd63e92b01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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47 <expand macro="citations"/>
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48 </tool>