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1 <tool id="bam_parallelism_test" name="BAM Parallelism Test" version="2.4.1">
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2 <description>
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3 BAM Parallelism Test
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4 </description>
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9
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5 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1" shared_inputs="" merge_outputs="outfile"></parallelism>
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6 <command>
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7
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5
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8 ln -s $normal input.bam;
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9 ln -s $normal.metadata.bam_index input.bam.bai;
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4
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10
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10
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11 touch $outfile;
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12
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12
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13 echo "HELLO";
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11
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14
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10
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15 cat $infile;
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16
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17 echo \$(cat $infile);
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18
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19 samtools view input.bam \$(cat $infile) | head -n 5 >> $outfile;
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20
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21 </command>
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22 <inputs>
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23 <param type="data" format="bam" name="normal" label="Normal Alignment BAM"/>
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4
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24
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25 <param type="data" format="txt" name="infile" label="Interval File"/>
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26 </inputs>
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27 <outputs>
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28 <data format="txt" name="outfile"/>
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29 </outputs>
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30 </tool> |
