Mercurial > repos > bebatut > metaphlan_2
changeset 1:1479a794253d draft default tip
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit d28e31b1b4dbcc3c406a4e8a5a41ac4576bf4f43-dirty
| author | bebatut |
|---|---|
| date | Tue, 02 Feb 2016 03:13:51 -0500 |
| parents | 8b151cff43e0 |
| children | |
| files | metaphlan2krona.xml |
| diffstat | 1 files changed, 65 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaphlan2krona.xml Tue Feb 02 03:13:51 2016 -0500 @@ -0,0 +1,65 @@ +<tool id="metaphlan2krona" name="Format MetaPhlAn2" version="0.1.0"> + + <description>output for Krona</description> + + <requirements> + <requirement type="package" version="2.2.5">bowtie2</requirement> + <requirement type="package" version="2.0">metaphlan2</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" description="" /> + <regex match="ERROR" + source="stderr" + level="fatal" + description="" /> + <regex match="WARNING" + source="stderr" + level="warning" + description="" /> + </stdio> + + <version_command> +<![CDATA[ +python \${METAPHLAN2_DIR}/utils/metaphlan2krona.py -v +]]> + </version_command> + + <command> +<![CDATA[ + python \${METAPHLAN2_DIR}/utils/metaphlan2krona.py + -p $input_file + -k $krona +]]> + </command> + + <inputs> + <param name="input_file" type="data" format="tabular,txt" label="Input + file (MetaPhlAN2 output)" help="(--profile)"/> + </inputs> + + <outputs> + <data format="tabular" name="krona" + label="${tool.name} on ${on_string}: Krona file" /> + </outputs> + + <tests> + </tests> + + <help><![CDATA[ + +**What it does** + +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/>`_. + +This tool format MetaPhlAn2 output for Krona. + + ]]></help> + + <citations> + <citation type="doi">10.1038/nmeth.3589</citation> + </citations> +</tool> \ No newline at end of file