Mercurial > repos > artbio > ngsplot

annotate runNGSplot.pl @ 0:3ca58369469c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
author artbio
date Wed, 06 Dec 2017 19:01:53 -0500
parents
children 4dd92ce61a5c
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0
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
1 #!/usr/bin/perl -w
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
2 use strict;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
3 use File::Basename 'dirname';
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
4 use File::Spec;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
5 use Cwd 'abs_path';
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
6
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
7 my @inputs = @ARGV;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
8 my @inputs2 = @inputs;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
9
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
10 my $genome_name = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
11 my $genomic_region_source_type__genomic_region = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
12 my $genomic_region_source_type__further_information = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
13 my $genomic_region_source_type__interval_size = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
14 my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_option = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
15 my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
16 my $numsamples = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
17 my $usepairs = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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18
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
19 #print STDERR "inputs @inputs\n";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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20
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
21 my $randfile = rand(100)."\.config\.txt";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
22 my $randfile2 = $randfile;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
23 $randfile2 =~ s/config\.txt/logfile/gm;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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24
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
25 my $outfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
26 open(FILE,">$outfile");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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27
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
28 for (my $i=1;$i<=$numsamples;$i++) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
29 my $bamfile=shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
30 my $reffile=shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
31 my $usegenelist=shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
32 my $genelist=shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
33 my $title=shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
34 my $fraglen=shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
35 my $color=shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
36 if ($usepairs eq 'yes') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
37 syswrite(FILE, "$bamfile\:$reffile\t$genelist\t$title\t$fraglen\t$color\n");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
38 }else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
39 syswrite(FILE, "$bamfile\t$genelist\t$title\t$fraglen\t$color\n");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
40 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
41 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
42 close(FILE);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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43
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
44 my $gene_database = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
45 my $randomly_sample = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
46 my $gene_order = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
47 my $knc = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
48 my $mit = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
49 my $nrs = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
50 my $chunk_size = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
51 my $quality_requirement = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
52 my $standard_error = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
53 my $radius_size = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
54 my $flooding_fraction = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
55 my $smooth_method = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
56 my $shaded_area = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
57 my $out_name = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
58 my $out_avg_name = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
59 my $out_hm_name = shift(@inputs);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
60
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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61
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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62 my $G = $genome_name;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
63 my $R = $genomic_region_source_type__genomic_region;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
64 my $C = $outfile;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
65 my $O = $out_name;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
66 my $O2 = $out_avg_name;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
67 my $O3 = $out_hm_name;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
68 my $F = $genomic_region_source_type__further_information;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
69 my $D = $gene_database;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
70 my $L = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
71 my $N = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
72 my $RB = $radius_size;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
73 my $S = $randomly_sample;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
74 my $CS = $chunk_size;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
75 my $MQ = $quality_requirement;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
76 my $IN = $genomic_region_source_type__interval_size;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
77 my $SE = $standard_error;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
78 my $MW = $smooth_method;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
79 my $H = $shaded_area;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
80 my $GO = $gene_order;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
81 my $KNC = $knc;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
82 my $MIT = $mit;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
83 my $NRS = $nrs;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
84 my $FC = $flooding_fraction;
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
85
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
86 if ($GO eq 'km') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
87 $GO = "$GO -KNC $KNC -MIT $MIT -NRS $NRS";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
88 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
89
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
90 my $logfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile2");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
91 open(FILE2,">>$logfile");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
92 my $cmd5="pwd >> $logfile 2>&1";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
93 system($cmd5);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
94 my $NGSPLOT = $ENV{"NGSPLOT"};
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
95 my $cmd='';
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
96 if (($R eq 'tss')||($R eq 'tes')) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
97 $cmd = "Rscript $NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
98 }elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_region_size') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
99 if ($IN eq 'automatic') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
100 $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
101 }else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
102 $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN >> $logfile 2>&1";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
103 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
104 }elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_floating_size') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
105 if ($IN eq 'automatic') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
106 $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
107 }else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
108 $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN >> $logfile 2>&1";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
109 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
110 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
111
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
112 print("$cmd\n");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
113 my $cmd2="cp data.zip $O";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
114 my $cmd3="rm $outfile";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
115 my $cmd4="rm $logfile";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
116 syswrite(FILE2, "\n$cmd\n");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
117 syswrite(FILE2, "\n$cmd2\n");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
118 syswrite(FILE2, "\n$cmd3\n");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
119 syswrite(FILE2, "\n$cmd4\n\n");
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
120
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
121 # print STDERR "cmd: $cmd\n";
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
122 system($cmd);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
123 system($cmd2);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
124 #system($cmd3);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
125 #system($cmd4);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
126
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
127 close(FILE2);
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
128
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
129