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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="2.5.2b">star</requirement>
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5 <requirement type="package" version="0.1.19">samtools</requirement>
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6 </requirements>
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7 </xml>
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8 <token name="@FASTQ_GZ_OPTION@">
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9 --readFilesCommand zcat
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10 </token>
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11 <xml name="citations">
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12 <citations>
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13 <citation type="doi">10.1093/bioinformatics/bts635</citation>
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14 </citations>
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15 </xml>
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16 <xml name="@SJDBOPTIONS@">
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17 <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"/>
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18 <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"/>
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19 </xml>
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20 </macros>
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