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1 #!/bin/bash
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2 #
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3 # Galaxy wrapper for BSMAP 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
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9 #get parameters
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10
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11 until [ $# -eq 0 ]
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12 do
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13 case $1 in
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14 input=*)
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15 input=${1#input=}
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16 ;;
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17 extract=*)
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18 extract=${1#extract=}
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19 ;;
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20 context=*)
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21 context=${1#context=}
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22 ;;
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23 depth=*)
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24 depth="cutoff=${1#depth=}"
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25 ;;
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26 cov_out=*)
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27 cov_out=${1#cov_out=}
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28 ;;
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29 meth_out=*)
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30 meth_out=${1#meth_out=}
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31 ;;
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32 esac
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33 shift
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34 done
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35
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36 case $extract in
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37 c)
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38 output="-cov_out=$cov_out";;
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39 m)
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40 output="-meth_out=$meth_out";;
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41 b)
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42 output="-meth_out=$meth_out -cov_out=$cov_out";;
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43 esac
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44
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45 if [ "$context" != "" ]
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46 then
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47 context="-context=$context"
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48 fi
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49
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50
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51 perl ~/dependencies/wig-parser/wiggle_extractor.pl -e $extract $context $output $input 2>&1>/dev/null |