<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.6.0b">star</requirement>
            <requirement type="package" version="1.8">samtools</requirement>
        </requirements>
    </xml>
    <token name="@FASTQ_GZ_OPTION@">
        --readFilesCommand zcat
    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/bts635</citation>
        </citations>
    </xml>
    <xml name="@SJDBOPTIONS@">
         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="true" help="Exon junction information for mapping splices"/>
         <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
    </xml>
    <xml name="dbKeyActions">
        <actions>
            <conditional name="refGenomeSource.geneSource">
                <when value="indexed">
                    <action type="metadata" name="dbkey">
                        <option type="from_data_table" name="rnastar_index2" column="1" offset="0">
                            <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                            <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
                        </option>
                    </action>
                </when>
                <when value="history">
                    <action type="metadata" name="dbkey">
                        <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
                    </action>
                </when>
            </conditional>
        </actions>
    </xml>
</macros>