annotate get_pdb.xml @ 0:2538366eb8fb draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb

<tool id="get_pdb" name="Get PDB file" version="0.1.0">
    <description>from Protein Data Bank</description>
    <requirements>
        <requirement type="package" version="1.20.1">wget</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        wget https://files.rcsb.org/download/${pdb_id}.pdb -O '$output'
    ]]></command>
    <inputs>
        <param name="pdb_id" type="text" label="PDB accession code">
            <validator type="regex" message="Invalid accession code">^[0-9][a-zA-Z0-9]{3}$</validator>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="pdb" />
    </outputs>
        <tests>
        <test>
            <param name="pdb_id" value="1AKI"/>
            <output name="output" file="1AKI.pdb"/>
        </test>
    </tests>
    <help><![CDATA[
        Download a protein structure in PDB format from the Protein Data Bank using its four-letter accession code.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/28.1.235</citation>
    </citations>
</tool>