Mercurial > repos > iuc > sarscov2summary

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
author iuc
date Mon, 04 May 2020 05:42:35 -0400
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<tool id="sarscov2summary" name="sarscov2summary" version="0.1" profile="18.01">
    <requirements>
        <requirement type="package" version="0.5">sarscov2summary</requirement>
    </requirements>
    <command><![CDATA[
sarscov2summary
-s '$slac'
-f '$fel'
-m '$meme'
-p '$prime'
-P $pvalue
-c '$coords'
-D '$db'
-d '$dups'
    ]]></command>
    <inputs>
        <param name ="slac" type="data" format="json" label="HyPhy SLAC Output" />
        <param name ="fel" type="data" format="json" label="HyPhy FEL Output" />
        <param name ="meme" type="data" format="json" label="HyPhy MEME Output" />
        <param name ="prime" type="data" format="json" label="HyPhy PRIME Output" />
        <param name="pvalue" type="float" value="0.1" label="P-value" />
        <param name="coords" type="data" format="fasta" label="Alignment With Reference" />
        <param name="db" type="data" format="json" label="Metadata" />
        <param name="dups" type="data" format="json" label="Duplicates" />
    </inputs>
    <outputs>
        <data name="summary" format="json" from_work_dir="summary.json" label="Summary" />
    </outputs>
    <tests>
        <test>
            <param name="slac" ftype="json" value="slac.json" />
            <param name="fel" ftype="json" value="fel.json" />
            <param name="meme" ftype="json" value="meme.json" />
            <param name="prime" ftype="json" value="prime.json" />
            <param name="coords" ftype="fasta" value="align.fasta" />
            <param name="db" ftype="json" value="meta.json" />
            <param name="dups" ftype="json" value="dups.json" />
            <output name="summary" ftype="json" compare="diff" value="summary.json" />
        </test>
    </tests>
        <help><![CDATA[
===============
sarscov2summary
===============

Custom summary script for the SARS-CoV2 Selection Analysis workflow. Takes HyPhy outputs as well as metadata to create final summary output.


    ]]></help>
    <citations>
        <citation type="bibtex">
            @misc{githubsarscov2summary,
            author = {Sergei Pond},
            year = {2020},
            title = {sarscov2summary},
            publisher = {Github},
            journal = {Github repository},
            url = {https://github.com/nickeener/sarscov2summary},
        }</citation>
    </citations>
</tool>