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1 #!/bin/sh
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2
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3 ### Galaxy Wrapper for BAMqc ###
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4
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5 alignment_files=""
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6 refgene=""
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7 attrID=""
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8 rRNA=""
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9 outputHTML=""
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10 stranded=""
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11 mapq="30"
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12 lowBound="-250"
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13 upperBound="250"
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14 stepSize="5"
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15 labels=""
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16 cores="1"
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17
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18 ARGS=$(getopt -o "r:f:R:o:s:p:q:" -- "$@")
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19
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20 if [ $? -ne 0 ]; then
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21 echo "Invalid command-line parameters. Do not use this script outside of Galaxy" >&2
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22 exit 1
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23 fi
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24
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25 eval set -- "$ARGS"
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26
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27 while [ $# -gt 0 ]; do
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28 case "$1" in
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29 -r)
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30 refgene="$2"
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31 shift 2
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32 ;;
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33 -f)
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34 attrID="$2"
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35 shift 2
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36 ;;
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37 -R)
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38 rRNA="$2"
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39 shift 2
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40 ;;
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41 -o)
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42 outputHTML=$2
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43 shift 2
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44 ;;
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45 -s)
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46 stranded=$2
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47 shift 2
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48 ;;
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49 -q)
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50 mapq=$2
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51 shift 2
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52 ;;
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53
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54 -p)
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55 cores=$2
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56 shift 2
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57 ;;
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58 --)
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59 shift
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60 break
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61 ;;
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62 esac
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63 done
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64
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65 if [ "$cores" -gt 10 ];then
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66 cores="10"
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67 fi
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68
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69 outputDir=`echo $outputHTML | sed 's/\.dat$/_files/'`
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70 if [ ! -d "$outputDir" ]; then
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71 mkdir $outputDir
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72 fi
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73
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74 touch bamqc.log
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75
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76 while [ "$#" -ne 0 ];
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77 do
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78 FILE="$1"
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79 LABEL=`echo $2 | sed 's/ /-/g; s/\[//; s/\]//;'`
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80 shift 2
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81 QNAME_SORTED=`samtools view -H ${FILE} | grep "SO:queryname"`
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82 if [ $? -ne 0 ]; then
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83 BASE=`basename ${FILE} \.dat`
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84 echo "Sorting BAM file (${LABEL}." >>samtools.log
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85 samtools sort -@ 5 -n ${FILE} ${BASE} 2>>samtools.log
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86 if [ $? -ne 0 ]; then
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87 echo "Error with samtools sorting for BAM file (${LABEL})." >&2
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88 cat samtools.log >&2
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89 exit 1
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90 fi
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91 echo "BAM file (${LABEL}) was re-sorted by query name." >>bamqc.log
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92 FILELIST="$FILELIST ${BASE}.bam"
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93 else
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94 FILELIST="$FILELIST $FILE"
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95 fi
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96 LABELLIST="$LABELLIST $LABEL"
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97 done
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98
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99 CMD="ezBAMQC -i $FILELIST -l $LABELLIST -f $attrID -r $refgene -o Galaxy_BAMqc_output --stranded $stranded -q $mapq --rRNA $rRNA -t $cores"
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100
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101 echo "BAMqc command: $CMD" >> bamqc.log
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102 echo >> bamqc.log
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103
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104 $CMD 2>> bamqc.log
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105
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106 if [ $? -ne 0 ]; then
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107 echo "BAMqc ran with errors" >&2
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108 cat bamqc.log >&2
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109 exit 1
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110 fi
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111
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112 sed -i "s/\.\.\/Galaxy_BAMqc_output\///g;" Galaxy_BAMqc_output/bamqc_output.html
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113
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114 cp -r Galaxy_BAMqc_output/data "$outputDir"
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115 cp -r Galaxy_BAMqc_output/figs "$outputDir"
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116 cp Galaxy_BAMqc_output/bamqc_output.html "$outputHTML"
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117
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118 if [ $? -ne 0 ]; then
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119 echo "Copying BAMqc results failed" >&2
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120 fi
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121
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122 echo "BAMqc results copied to $outputDir" >>bamqc.log
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