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1 #!/bin/sh
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2 #
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3 # Wrapper script to run RnaChipIntegrator as a Galaxy tool
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4 #
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5 # usage: sh rnachipintegrator_wrapper.sh [OPTIONS] <rnaseq_in> <chipseq_in> --output_xls <xls_out>
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6 #
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7 echo RnaChipIntegrator: analyse gene and peak data
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8 #
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9 # Collect command line options
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10 opts=
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11 xlsx_file=
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12 zip_file=
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13 gene_centric=
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14 peak_centric=
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15 gene_centric_summary=
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16 peak_centric_summary=
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17 while [ ! -z "$1" ] ; do
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18 case $1 in
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19 --xlsx_file)
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20 shift; xlsx_file=$1
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21 opts="$opts --xlsx"
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22 ;;
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23 --output_files)
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24 shift; gene_centric=$1
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25 shift; peak_centric=$1
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26 ;;
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27 --summary_files)
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28 shift; gene_centric_summary=$1
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29 shift; peak_centric_summary=$1
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30 opts="$opts --summary"
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31 ;;
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32 --zip_file)
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33 shift; zip_file=$1
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34 ;;
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35 *)
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36 opts="$opts $1"
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37 ;;
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38 esac
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39 shift
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40 done
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41 #
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42 # Run RnaChipIntegrator
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43 # NB append stderr to stdout otherwise Galaxy job will fail
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44 # Direct output to a temporary directory
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45 outdir=$(mktemp -d)
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46 base_name=galaxy
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47 cmd="RnaChipIntegrator --name=${outdir}/${base_name} $opts"
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48 echo $cmd
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49 $cmd 2>&1
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50 #
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51 # Check exit code
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52 exit_status=$?
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53 if [ "$exit_status" -ne "0" ] ; then
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54 echo RnaChipIntegrator exited with non-zero status >&2
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55 # Clean up and exit
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56 /bin/rm -rf $outdir
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57 exit $exit_status
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58 fi
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59 #
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60 # Deal with output XLSX file
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61 if [ -f "${outdir}/${base_name}.xlsx" ] ; then
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62 /bin/mv ${outdir}/${base_name}.xlsx $xlsx_file
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63 else
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64 echo No file ${outdir}/${base_name}.xlsx >&2
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65 # Clean up and exit
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66 /bin/rm -rf $outdir
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67 exit 1
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68 fi
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69 #
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70 # Generate zip file
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71 if [ ! -z "$zip_file" ] ; then
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72 for ext in \
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73 gene_centric \
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74 gene_centric_summary \
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75 peak_centric \
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76 peak_centric_summary ; do
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77 txt_file=${outdir}/${base_name}_${ext}.txt
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78 if [ -f "$txt_file" ] ; then
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79 zip -j -g ${outdir}/archive.zip $txt_file
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80 fi
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81 done
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82 /bin/mv ${outdir}/archive.zip $zip_file
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83 fi
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84 #
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85 # Collect tab delimited files
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86 for ext in \
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87 gene_centric \
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88 gene_centric_summary \
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89 peak_centric \
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90 peak_centric_summary ; do
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91 eval dest=\$$ext
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92 if [ ! -z "$dest" ] ; then
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93 outfile=${outdir}/${base_name}_${ext}.txt
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94 if [ -f "$outfile" ] ; then
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95 /bin/mv $outfile $dest
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96 else
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97 echo ERROR missing output file $outfile >&2
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98 fi
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99 fi
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100 done
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101 #
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102 # Clean up
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103 /bin/rm -rf $outdir
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104 #
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105 # Done
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