annotate bsmap_meth_caller.sh @ 18:765fe3947e2a draft

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author eiriche
date Mon, 03 Dec 2012 02:38:16 -0500
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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 #get parameters
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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=${1#tempdir=}
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24 ;;
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25 ref=*)
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26 ref=${1#ref=}
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27 ;;
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28 esac
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29 shift
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30 done
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31
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32 methratio.py -o $output -d $ref -q $input