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1 #!/usr/bin/perl
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2 use strict;
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3 use Getopt::Long;
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4 use vars qw($opt_reference $opt_output @opt_input $opt_genomes $opt_source $opt_datasource $opt_fields $opt_nocalls $opt_calibration $opt_jctscore $opt_jctside $opt_jctdistance $opt_jctlength $opt_jctpriority $opt_jcttumor);
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5 $| = 1; # set autoflush to screen
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6
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7 # This is a wrapper for the cgatools mkvcf function to run cgatools mkvcf in Galaxy.
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8 # written 8-10-2012 by bcrain@completegenomics.com
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9
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10 #print join("\n", @ARGV), "\n";
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11 &GetOptions("reference=s", "output=s", "input=s@", "genomes=i", "source=s", "datasource=s", "fields=s", "nocalls", "calibration:s", "jctscore=i", "jctside=i", "jctdistance=i", "jctlength=i", "jctpriority", "jcttumor");
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12
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13 my $command = "cgatools mkvcf --beta --reference $opt_reference --output $opt_output --source-names $opt_source";
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14
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15 if ($opt_datasource eq 'in')
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16 {
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17 foreach my $file (@opt_input)
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18 {
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19 if ($opt_source eq 'masterVar') {$command .= " --master-var ";}
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20 elsif ($opt_source eq 'SV') {$command .= " --junction-file ";}
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21 else {die "there is an error in the logic: wrong source $opt_source for datasource $opt_datasource.\n";}
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22 $command .= $file
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23 }
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24 }
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25 elsif ($opt_datasource eq 'out')
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26 {
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27 if ($opt_genomes == 1)
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28 {
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29 if ($opt_input[0] =~ m/masterVar/ and $opt_source eq 'masterVar')
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30 {
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31 -f $opt_input[0] or die "$opt_input[0] is not a valid file.\n";
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32 $command .= " --master-var $opt_input[0]";
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33 }
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34 elsif ($opt_input[0] =~ m/Junctions/ and $opt_source eq 'SV')
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35 {
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36 -f $opt_input[0] or die "$opt_input[0] is not a valid file.\n";
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37 $command .= " --junction-file $opt_input[0]";
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38 }
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39 else
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40 {
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41 $opt_input[0] =~ s/\/$//;
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42 -d $opt_input[0] or die "$opt_input[0] is not a valid directory.\n";
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43 $command .= " --genome-root $opt_input[0]";
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44 }
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45 }
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46 else
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47 {
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48 -T $opt_input[0] or die "$opt_input[0] is not a valid file.\n";
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49 my $count = 0;
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50 foreach my $file (split /\s+/, `cat $opt_input[0]`)
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51 {
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52 $count ++;
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53 ($opt_genomes == 2 and $count > 2) and die "The number of inputs in your list file cannot be greater than the number of genomes selected.\n";
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54 if ($file =~ m/masterVar/ and $opt_source eq 'masterVar')
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55 {
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56 -f $file or die "$file is not a valid file.\n";
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57 $command .= " --master-var ";
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58 }
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59 elsif ($file =~ m/Junctions/ and $opt_source eq 'SV')
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60 {
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61 -f $file or die "$file is not a valid file.\n";
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62 $command .= " --junction-file ";
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63 }
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64 else
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65 {
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66 -d $file or die "$file is not a valid directory.\n";
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67 $command .= " --genome-root ";
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68 }
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69 $command .= $file
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70 }
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71 }
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72 }
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73 else
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74 {die "there is an error in the logic: wrong datasource $opt_datasource.\n";}
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75
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76 if ($opt_calibration)
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77 {
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78 (-r "$opt_calibration/0.0.0/metrics.tsv" or -r "$opt_calibration/version0.0.0/metrics.tsv") or die "This folder does not contain the calibration data\n";
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79 $command .= " --calibration-root $opt_calibration";
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80 }
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81
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82 $opt_fields eq 'all' or $command .= " --field-names $opt_fields";
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83 $opt_nocalls and $command .= " --include-no-calls";
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84 $opt_jctscore and $command .= " --junction-score-threshold $opt_jctscore";
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85 $opt_jctside and $command .= " --junction-side-length-threshold $opt_jctside";
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86 $opt_jctdistance and $command .= " --junction-distance-tolerance $opt_jctdistance";
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87 $opt_jctlength and $command .= " --junction-length-threshold $opt_jctlength";
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88 $opt_jctpriority and $command .= " --junction-normal-priority";
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89 $opt_jcttumor and $command .= " --junction-tumor-hc";
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90
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91 my $version = `cgatools | head -1`;
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92 print "$version\n";
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93 print "$command \n";
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94
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95 `$command`; |
