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31
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1 #!/bin/bash
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2 #
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3 # Galaxy wrapper for WIG parser
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4 # Written by Eugen Eirich @ Institute of Molecular Biology Mainz
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5 #
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6
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7 set -e
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8
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9
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10 #get parameters
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11
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12 until [ $# -eq 0 ]
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13 do
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14 case $1 in
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15 input=*)
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16 input=${1#input=}
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17 ;;
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18 extract=*)
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19 extract=${1#extract=}
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20 ;;
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21 context=*)
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22 context=${1#context=}
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23 ;;
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24 depth=*)
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25 depth="cutoff=${1#depth=}"
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26 ;;
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27 cov_out=*)
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28 cov_out=${1#cov_out=}
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29 ;;
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30 meth_out=*)
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31 meth_out=${1#meth_out=}
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32 ;;
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33 esac
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34 shift
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35 done
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36
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37 case $extract in
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38 c)
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39 output="-cov_out=$cov_out";;
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40 m)
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41 output="-meth_out=$meth_out";;
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42 b)
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43 output="-meth_out=$meth_out -cov_out=$cov_out";;
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44 esac
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45
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46 if [ "$context" != "" ]
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47 then
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48 context="-context=$context"
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49 fi
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50
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51 cd "$(dirname ${BASH_SOURCE[0]})"
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52 perl wig_extractor.pl -e $extract $context $output $input 2>&1>/dev/null
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