view sra_macros.xml @ 1:462ee06c9358 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede

<macros>
    <macro name="requirements">
        <requirements>
            <requirement type="package" version="1.2.3">ngs_sdk</requirement>
            <requirement type="package" version="2.6.2">ncbi_vdb</requirement>
            <requirement type="package" version="2.6.2">sra_toolkit</requirement>
            <requirement type="package" version="2.6.2">sra-tools</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>
                <option value="file_list">List of SRA accession, one per line</option>
            </param>
            <when value="accession_number">
                <param name="accession" type="text" label="SRR accession" help="Must start with SRR,DRR or ERR, e.g. SRR925743 , ERR343809"/>
            </when>
            <when value="file">
                <param format="sra" name="file" type="data" label="sra archive"/>
            </when>
            <when value="file_list">
                <param format="txt" name="file_list" type="data" label="sra accession list"/>
            </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. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)."/>
    </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>
    <macro name="citation">
        <citations>
            <citation type="doi">10.1093/nar/gkq1019</citation>
        </citations>
    </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).

        Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ). 
        
        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/galaxyproject/tools-iuc.
        
    </token>
</macros>