Mercurial > repos > bebatut > metaphlan2
comparison metaphlan2krona.xml @ 25:e8e0f835b4b6 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
| author | bebatut |
|---|---|
| date | Thu, 31 Mar 2016 03:25:48 -0400 |
| parents | |
| children | 3f52f2d65d41 |
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| 24:51e7d53fcefb | 25:e8e0f835b4b6 |
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| 1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="0.1.0"> | |
| 2 | |
| 3 <description>output for Krona</description> | |
| 4 | |
| 5 <requirements> | |
| 6 <requirement type="package" version="2.2.5">bowtie2</requirement> | |
| 7 <requirement type="package" version="2.0">metaphlan2</requirement> | |
| 8 </requirements> | |
| 9 | |
| 10 <stdio> | |
| 11 <exit_code range="1:" level="fatal" description="" /> | |
| 12 <regex match="ERROR" | |
| 13 source="stderr" | |
| 14 level="fatal" | |
| 15 description="" /> | |
| 16 <regex match="WARNING" | |
| 17 source="stderr" | |
| 18 level="warning" | |
| 19 description="" /> | |
| 20 </stdio> | |
| 21 | |
| 22 <version_command> | |
| 23 <![CDATA[ | |
| 24 python \${METAPHLAN2_DIR}/utils/metaphlan2krona.py -v | |
| 25 ]]> | |
| 26 </version_command> | |
| 27 | |
| 28 <command> | |
| 29 <![CDATA[ | |
| 30 python \${METAPHLAN2_DIR}/utils/metaphlan2krona.py | |
| 31 -p $input_file | |
| 32 -k $krona | |
| 33 ]]> | |
| 34 </command> | |
| 35 | |
| 36 <inputs> | |
| 37 <param name="input_file" type="data" format="tabular,txt" label="Input | |
| 38 file (MetaPhlAN2 output)" help="(--profile)"/> | |
| 39 </inputs> | |
| 40 | |
| 41 <outputs> | |
| 42 <data format="tabular" name="krona" | |
| 43 label="${tool.name} on ${on_string}: Krona file" /> | |
| 44 </outputs> | |
| 45 | |
| 46 <tests> | |
| 47 </tests> | |
| 48 | |
| 49 <help><![CDATA[ | |
| 50 | |
| 51 **What it does** | |
| 52 | |
| 53 MetaPhlAn is a computational tool for profiling the composition of microbial | |
| 54 communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun | |
| 55 sequencing data with species level resolution. For more information, check the | |
| 56 `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_. | |
| 57 | |
| 58 This tool format MetaPhlAn2 output for Krona. | |
| 59 | |
| 60 ]]></help> | |
| 61 | |
| 62 <citations> | |
| 63 <citation type="doi">10.1038/nmeth.3589</citation> | |
| 64 </citations> | |
| 65 </tool> |