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11
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1 #!/bin/bash
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2 #
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3 # Galaxy wrapper for Bismark Methylation Caller
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4 #
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5
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6 set -e
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7
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8 #get parameters
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9
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10 until [ $# -eq 0 ]
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11 do
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12 case $1 in
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13 input=*)
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14 input=${1#input=}
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15 ;;
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16 method=*)
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17 method=${1#method=}
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18 ;;
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19 output=*)
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20 output=${1#output=}
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21 ;;
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22 tempdir=*)
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23 tempdir=${1#tempdir=}
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24 ;;
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25 esac
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26 shift
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27 done
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28 (grep ^@ $input; grep -v ^@ $input | sort -k3,3 -k1,1) > $tempdir"bismark_sam_sorted.sam"
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29 methylation_extractor -$method -o $output $tempdir"bismark_sam_sorted.sam" 2>&1 > /dev/null
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30
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31
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32
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33
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34
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35
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