annotate bsmap_wrapper.sh @ 19:e3e36b45c1da draft

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author eiriche
date Mon, 03 Dec 2012 02:38:26 -0500
parents 91e88de226a3
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3
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1 #!/bin/bash
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2 #
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3 # Galaxy wrapper for BSMAP
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4 # Written by Eugen Eirich @ Institute for 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 #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 $1 in
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14 ref=*)
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15 ref=${1#ref=}
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16 ;;
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17 library=*)
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18 library=${1#library=}
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19 ;;
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20 unpaired=*)
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21 unpaired=${1#unpaired=}
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22 ;;
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23 mapped=*)
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24 mapped=${1#mapped=}
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25 ;;
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26 fullparam=*)
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27 fullparam=${1#fullparam=}
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28 ;;
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29 mate1=*)
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30 mate1=${1#mate1=}
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31 ;;
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32 mate2=*)
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33 mate2=${1#mate2=}
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34 ;;
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35 qual=*)
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36 qual="-z ${1#qual=}"
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37 ;;
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38 threshold=*)
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39 threshold="-q ${1#threshold=}"
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40 ;;
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41 lowqual=*)
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42 lowqual="-f ${1#lowqual=}"
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43 ;;
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44 adapter=*)
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45 adapter=${1#adapter=}
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46 ;;
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47 firstn=*)
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48 firstn="-L ${1#firstn=}"
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49 ;;
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50 repeat_reads=*)
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51 repeat_reads="-r ${1#repeat_reads=}"
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52 ;;
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53 seed_size=*)
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54 seed_size="-s ${1#seed_size=}"
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55 ;;
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56 mismatch=*)
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57 mismatch="-v ${1#mismatch=}"
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58 ;;
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59 equal_best=*)
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60 equal_best="-w ${1#equal_best=}"
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61 ;;
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62 start=*)
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63 start="-B ${1#start=}"
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64 ;;
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65 end=*)
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66 end="-E ${1#end=}"
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67 ;;
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68 index_interval=*)
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69 index_interval="-I ${1#index_interval=}"
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70 ;;
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71 seed_random=*)
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72 seed_random=${1#seed_random=}
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73 ;;
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74 rrbs=*)
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75 rrbs=${1#rrbs=}
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76 ;;
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77 mode=*)
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78 mode="-n ${1#mode=}"
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79 ;;
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80 align_info=*)
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81 align_info=${1#align_info=}
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82 ;;
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83 maxinsert=*)
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84 maxinsert="-x ${1#maxinsert=}"
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85 ;;
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86 mininsert=*)
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87 mininsert="-m ${1#mininsert=}"
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88 ;;
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89 summary=*)
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90 summary=${1#summary=}
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91 ;;
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92 esac
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93 shift
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94 done
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95
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96
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97 if [ "$rrbs" != "" ]
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98 then
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99 rrbs="-D $rrbs"
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100 fi
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101
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102 if [ "$align_info" != "" ]
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103 then
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104 align_info="-M $align_info"
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105 fi
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106
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107 if [ "$adapter" != "" ]
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108 then
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109 adapter="-A $adapter"
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110 fi
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111
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112 if [ "$seed_random" != "" ]
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113 then
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114 seed_random="-S $seed_random"
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115 fi
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116
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117
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118 if [ "$library" == "single" ]
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119 then
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120 if [ "$fullparam" == 'false' ]
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121 then
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122 bsmap -a $mate1 -d $ref -o $mapped -R -r 0 -p 4 > $summary
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123 else
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124 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 > $summary
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125 fi
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126 else
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127 if [ "$fullparam" == 'false' ]
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128 then
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129 bsmap -a $mate1 -b $mate2 -2 $unpaired -d $ref -o $mapped -R -r 0 -p 4 > $summary
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130 else
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131 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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132 fi
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133 fi