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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
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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=${1#library=}
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19 ;;
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20 fullparam=*)
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21 fullparam=${1#fullparam=}
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22 ;;
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23 mate1=*)
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24 mate1=${1#mate1=}
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25 ;;
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26 mate2=*)
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27 mate2=${1#mate2=}
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28 ;;
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29 qual=*)
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30 qual=${1#qual=}
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31 ;;
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32 seedmms=*)
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33 seedmms="--seedmms ${1#seedmms=}"
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34 ;;
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35 seedlen=*)
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36 seedlen="--seedlen ${1#seedlen=}"
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37 ;;
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38 maqerr=*)
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39 maqerr="--maqerr ${1#maqerr=}"
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40 ;;
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41 directional=*)
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42 directional=${1#directional=}
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43 ;;
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44 header=*)
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45 header=${1#header=}
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46 ;;
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47 minins=*)
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48 minins="--minins ${1#minins=}"
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49 ;;
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50 maxins=*)
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51 maxins="--maxins ${1#maxins=}"
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52 ;;
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53 mapped=*)
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54 mapped=${1#mapped=}
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55 ;;
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56 summary=*)
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57 summary=${1#summary=}
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58 ;;
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59 tempdir=*)
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60 tempdir=${1#tempdir=}
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61 ;;
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62 esac
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63 shift
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64 done
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65
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66
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67 if [ "$library" == "single" ]
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68 then
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69 if [ "$fullparam" == 'false' ]
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70 then
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71 bismark --output_dir $tempdir --temp_dir $tempdir --quiet $ref $mate1 2>&1 > /dev/null
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72 else
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73 bismark --output_dir $tempdir --temp_dir $tempdir --quiet $qual $seedmms $seedlen $maqerr $directional $header $ref $mate1 2>&1 > /dev/null
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74 fi
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75 else
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76 if [ "$fullparam" == 'false' ]
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77 then
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78 bismark --output_dir $tempdir --temp_dir $tempdir --quiet $ref -1 $mate1 -2 $mate2 2>&1 > /dev/null
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79 else
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80 bismark --output_dir $tempdir --temp_dir $tempdir --quiet $qual $seedmms $seedlen $maqerr $directional $header $minins $maxins $ref -1 $mate1 -2 $mate2 2>&1 > /dev/null
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81 fi
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82 fi
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83
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84
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85 #call bismark. output in temp-directory (files_path)
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86
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87
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88 #parse the filename of the input -> same as output
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89 IFS="/"
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90 set - $mate1
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91 outfile=${*:$#:1}
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92
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93 #sort the mapped reads by chromosome
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94 #sort -k 3,3 -k 4,4n "$tempdir/${outfile}_bismark_pe.sam" > "$tempdir/${outfile}_bismark_pe_sorted.sam"
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95
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96 #copy resultfiles back into galaxy
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97 #cp "$tempdir/${outfile}_bismark_sorted.sam" "$mapped"
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98 if [ "$library" == "single" ]
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99 then
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100 cp "$tempdir/${outfile}_bismark.sam" "$mapped"
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101 cp "$tempdir/${outfile}_Bismark_mapping_report.txt" "$summary"
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102 else
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103 cp "$tempdir/${outfile}_bismark_pe.sam" "$mapped"
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104 cp "$tempdir/${outfile}_Bismark_paired-end_mapping_report.txt" "$summary"
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105 fi
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106
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107
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108
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109
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110
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111
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112
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