Mercurial > repos > thanhlv > coverm
changeset 0:ef0187f2d1f6 draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/coverm commit a0be3607cd2a8b0d3bf6cdab4c9c50703936f941
| author | thanhlv |
|---|---|
| date | Tue, 08 Oct 2019 13:54:30 -0400 |
| parents | |
| children | 26c496578cc6 |
| files | coverm.xml |
| diffstat | 1 files changed, 35 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coverm.xml Tue Oct 08 13:54:30 2019 -0400 @@ -0,0 +1,35 @@ +<tool id="coverm" name="coverm" version="@VERSION@"> + <description>Read coverage calculator for metagenomics</description> + <macros> + <token name="@VERSION@">0.2.0.alpha7</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">coverm</requirement> + </requirements> + <version_command>coverm --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + coverm contigs + -t \${GALAXY_SLOTS} + --methods metabat + --bam-files $bam + > depth.tsv + ]]></command> + + <inputs> + <param name="bam" type="data" format="bam" label="Input bam file" /> + </inputs> + + <outputs> + <data name="depth" format="json" label="{tool.name} on ${on_string} Depth" from_work_dir="depth.tsv"/> + </outputs> + + <tests> + <test> + </test> + </tests> + <help><![CDATA[ + + Documentation can be found at `<https://github.com/wwood/CoverM>`_. + + ]]></help> +</tool>