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1 #!/bin/bash
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2 #
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3 # Galaxy wrapper for Bismark
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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 $1 in
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13 ref=*)
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14 ref=${1#ref=}
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15 ;;
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16 library=*)
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17 library=${1#library=}
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18 ;;
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19 unpaired=*)
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20 unpaired=${1#unpaired=}
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21 ;;
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22 mapped=*)
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23 mapped=${1#mapped=}
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24 ;;
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25 fullparam=*)
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26 fullparam=${1#fullparam=}
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27 ;;
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28 mate1=*)
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29 mate1=${1#mate1=}
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30 ;;
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31 mate2=*)
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32 mate2=${1#mate2=}
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33 ;;
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34 qual=*)
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35 qual="-z ${1#qual=}"
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36 ;;
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37 threshold=*)
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38 threshold="-q ${1#threshold=}"
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39 ;;
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40 lowqual=*)
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41 lowqual="-f ${1#lowqual=}"
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42 ;;
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43 adapter=*)
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44 adapter=${1#adapter=}
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45 ;;
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46 firstn=*)
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47 firstn="-L ${1#firstn=}"
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48 ;;
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49 repeat_reads=*)
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50 repeat_reads="-r ${1#repeat_reads=}"
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51 ;;
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52 seed_size=*)
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53 seed_size="-s ${1#seed_size=}"
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54 ;;
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55 mismatch=*)
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56 mismatch="-v ${1#mismatch=}"
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57 ;;
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58 equal_best=*)
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59 equal_best="-w ${1#equal_best=}"
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60 ;;
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61 start=*)
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62 start="-B ${1#start=}"
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63 ;;
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64 end=*)
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65 end="-E ${1#end=}"
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66 ;;
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67 index_interval=*)
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68 index_interval="-I ${1#index_interval=}"
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69 ;;
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70 seed_random=*)
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71 seed_random=${1#seed_random=}
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72 ;;
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73 rrbs=*)
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74 rrbs=${1#rrbs=}
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75 ;;
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76 mode=*)
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77 mode="-n ${1#mode=}"
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78 ;;
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79 align_info=*)
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80 align_info=${1#align_info=}
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81 ;;
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82 maxinsert=*)
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83 maxinsert="-x ${1#maxinsert=}"
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84 ;;
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85 mininsert=*)
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86 mininsert="-m ${1#mininsert=}"
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87 ;;
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88 summary=*)
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89 summary=${1#summary=}
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90 ;;
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91 esac
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92 shift
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93 done
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94
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95
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96 if [ "$rrbs" != "" ]
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97 then
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98 rrbs="-D $rrbs"
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99 fi
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100
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101 if [ "$align_info" != "" ]
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102 then
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103 align_info="-M $align_info"
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104 fi
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105
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106 if [ "$adapter" != "" ]
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107 then
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108 adapter="-A $adapter"
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109 fi
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110
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111 if [ "$seed_random" != "" ]
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112 then
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113 seed_random="-S $seed_random"
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114 fi
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115
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116
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117 if [ "$library" == "single" ]
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118 then
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119 if [ "$fullparam" == 'false' ]
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120 then
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121 bsmap -a $mate1 -d $ref -o $mapped -R -r 0 -p 4 > $summary
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122 else
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123 bsmap -a $mate1 -d $ref -o $mapped -R -r 0 -p 4 $qual $threshold $lowqual $adapter $firstn $repeat_reads $seed_size $mismatch $equal_best $start $end $index_interval $mode > $summary
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124 fi
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125 else
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126 if [ "$fullparam" == 'false' ]
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127 then
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128 bsmap -a $mate1 -b $mate2 -2 $unpaired -d $ref -o $mapped -R -r 0 -p 4 > $summary
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129 else
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130 bsmap -a $mate1 -b $mate2 -2 $unpaired -d $ref -o $mapped -R -r 0 -p 4 $qual $threshold $lowqual $adapter $firstn $repeat_reads $seed_size $mismatch $equal_best $start $end $index_interval $mode $maxinsert $mininsert > $summary
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131 fi
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132 fi
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