view sra_macros.xml @ 0:9f74a22d2060 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty

<macros>
    <macro name="requirements">
        <requirements>
            <requirement type="package" version="1.1.3">ngs_sdk</requirement>
            <requirement type="package" version="2.5.2">ncbi_vdb</requirement>
            <requirement type="package" version="2.5.2">sra_toolkit</requirement>
            <requirement type="package" version="3">ascp</requirement>
            <requirement type="package" version="5.18.1">perl</requirement>
        </requirements>
    </macro>
    <macro name="input_conditional">
        <conditional name="input">
            <param name="input_select" type="select" label="select input type">
                <option value="accession_number">SRR accession</option>
                <option value="file">SRA archive in current history</option>
            </param>
            <when value="accession_number">
                <param name="accession" type="text" label="accession"/>
            </when>
            <when value="file">
                <param format="sra" name="file" type="data" label="sra archive"/>
            </when>
        </conditional>
    </macro>
    <macro name="alignments">
        <param name="alignments" type="select" value="both">
            <label>aligned or unaligned reads</label>
            <option value="both">both</option>
            <option value="aligned">aligned only</option>
            <option value="unaligned">unaligned only</option>
        </param>
    </macro>
    <macro name="minMapq">
        <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/>
    </macro>
    <macro name="region">
        <param format="text" name="region" type="text" label="aligned region" optional="true"
               help="Filter by position on genome. Name can  either be accession.version (ex: NC_000001.10) or file specific name (ex:chr1 or 1). from and to are 1-based coordinates"/>
    </macro>
    <macro name="matepairDist">
        <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
               help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference"/>
    </macro>
    <token name="@SRATOOLS_ATTRRIBUTION@">Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
        Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
        Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
        For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/mdshw5/sra-tools-galaxy.</token>
</macros>