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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 export PATH="/home/galaxy/dependencies/bismark:$PATH"
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9 export PATH="/home/galaxy/dependencies/diverse:$PATH"
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10
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11 #get parameters
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12
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13 until [ $# -eq 0 ]
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14 do
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15 case $1 in
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16 ref=*)
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17 ref=${1#ref=}
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18 ;;
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19 library=*)
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20 library=${1#library=}
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21 ;;
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22 fullparam=*)
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23 fullparam=${1#fullparam=}
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24 ;;
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25 mate1=*)
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26 mate1=${1#mate1=}
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27 ;;
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28 mate2=*)
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29 mate2=${1#mate2=}
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30 ;;
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31 qual=*)
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32 qual=${1#qual=}
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33 ;;
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34 seedmms=*)
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35 seedmms="--seedmms ${1#seedmms=}"
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36 ;;
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37 seedlen=*)
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38 seedlen="--seedlen ${1#seedlen=}"
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39 ;;
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40 maqerr=*)
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41 maqerr="--maqerr ${1#maqerr=}"
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42 ;;
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43 directional=*)
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44 directional=${1#directional=}
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45 ;;
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46 header=*)
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47 header=${1#header=}
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48 ;;
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49 minins=*)
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50 minins="--minins ${1#minins=}"
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51 ;;
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52 maxins=*)
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53 maxins="--maxins ${1#maxins=}"
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54 ;;
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55 mapped=*)
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56 mapped=${1#mapped=}
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57 ;;
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58 summary=*)
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59 summary=${1#summary=}
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60 ;;
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61 tempdir=*)
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62 tempdir=${1#tempdir=}
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63 ;;
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64 esac
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65 shift
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66 done
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67
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68
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69 if [ "$library" == "single" ]
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70 then
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71 if [ "$fullparam" == 'false' ]
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72 then
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73 bismark --output_dir $tempdir --temp_dir $tempdir --quiet $ref $mate1 2>&1 > /dev/null
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74 else
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75 bismark --output_dir $tempdir --temp_dir $tempdir --quiet $qual $seedmms $seedlen $maqerr $directional $header $ref $mate1 2>&1 > /dev/null
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76 fi
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77 else
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78 if [ "$fullparam" == 'false' ]
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79 then
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80 bismark --output_dir $tempdir --temp_dir $tempdir --quiet $ref -1 $mate1 -2 $mate2 2>&1 > /dev/null
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81 else
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82 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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83 fi
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84 fi
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85
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86
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87 #call bismark. output in temp-directory (files_path)
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88
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89
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90 #parse the filename of the input -> same as output
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91 IFS="/"
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92 set - $mate1
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93 outfile=${*:$#:1}
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94
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95 #sort the mapped reads by chromosome
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96 #sort -k 3,3 -k 4,4n "$tempdir/${outfile}_bismark_pe.sam" > "$tempdir/${outfile}_bismark_pe_sorted.sam"
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97
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98 #copy resultfiles back into galaxy
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99 #cp "$tempdir/${outfile}_bismark_sorted.sam" "$mapped"
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100 if [ "$library" == "single" ]
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101 then
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102 cp "$tempdir/${outfile}_bismark.sam" "$mapped"
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103 cp "$tempdir/${outfile}_Bismark_mapping_report.txt" "$summary"
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104 else
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105 cp "$tempdir/${outfile}_bismark_pe.sam" "$mapped"
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106 cp "$tempdir/${outfile}_Bismark_paired-end_mapping_report.txt" "$summary"
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107 fi
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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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113
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114
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