diff ngsplot_galaxytoolshed_v.10/ngsplot_main/runNGSplot.pl @ 12:f7debdafc7cb draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed_v.10/ngsplot_main/runNGSplot.pl	Tue Mar 31 10:15:27 2015 -0400
@@ -0,0 +1,126 @@
+#!/usr/bin/perl -w
+use strict;
+use File::Basename 'dirname';
+use File::Spec;
+use Cwd 'abs_path';
+
+my @inputs = @ARGV;
+my @inputs2 = @inputs;
+
+my $genome_name = shift(@inputs);
+my $genomic_region_source_type__genomic_region = shift(@inputs);
+my $genomic_region_source_type__further_information = shift(@inputs);
+my $genomic_region_source_type__interval_size = shift(@inputs);
+my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_option = shift(@inputs);
+my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size = shift(@inputs);
+my $numsamples = shift(@inputs);
+my $usepairs = shift(@inputs);
+
+#print STDERR "inputs @inputs\n";
+
+my $randfile = rand(100)."\.config\.txt";
+my $randfile2 = $randfile;
+$randfile2 =~ s/config\.txt/logfile/gm;
+
+my $outfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile");
+open(FILE,">$outfile");
+
+for (my $i=1;$i<=$numsamples;$i++) {
+   my $bamfile=shift(@inputs);
+   my $reffile=shift(@inputs);
+   my $usegenelist=shift(@inputs);
+   my $genelist=shift(@inputs);
+   my $title=shift(@inputs);
+   my $fraglen=shift(@inputs);
+   my $color=shift(@inputs);   
+   if ($usepairs eq 'yes') {
+      syswrite(FILE, "$bamfile\:$reffile\t$genelist\t$title\t$fraglen\t$color\n");
+   }else {
+      syswrite(FILE, "$bamfile\t$genelist\t$title\t$fraglen\t$color\n");
+   }
+}
+close(FILE);
+
+my $gene_database = shift(@inputs);
+my $randomly_sample = shift(@inputs);
+my $gene_order = shift(@inputs);
+my $knc = shift(@inputs);
+my $mit = shift(@inputs);
+my $nrs = shift(@inputs);
+my $chunk_size = shift(@inputs);
+my $quality_requirement = shift(@inputs);
+my $standard_error = shift(@inputs);
+my $radius_size = shift(@inputs);
+my $flooding_fraction = shift(@inputs);
+my $smooth_method = shift(@inputs);
+my $shaded_area = shift(@inputs);
+my $out_name = shift(@inputs);
+my $out_avg_name = shift(@inputs);
+my $out_hm_name = shift(@inputs);
+
+
+my $G = $genome_name;
+my $R = $genomic_region_source_type__genomic_region;
+my $C = $outfile;
+my $O = $out_name;
+my $O2 = $out_avg_name;
+my $O3 = $out_hm_name;
+my $F = $genomic_region_source_type__further_information;
+my $D = $gene_database;
+my $L = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size;
+my $N = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size;
+my $RB = $radius_size;
+my $S = $randomly_sample;
+my $CS = $chunk_size;
+my $MQ = $quality_requirement;
+my $IN = $genomic_region_source_type__interval_size;
+my $SE = $standard_error;
+my $MW = $smooth_method;
+my $H = $shaded_area;
+my $GO = $gene_order;
+my $KNC = $knc;
+my $MIT = $mit;
+my $NRS = $nrs;
+my $FC = $flooding_fraction;
+
+if ($GO eq 'km') {
+   $GO = "$GO -KNC $KNC -MIT $MIT -NRS $NRS";
+}
+
+my $logfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile2");
+open(FILE2,">>$logfile");
+my $cmd5="pwd >> $logfile 2>&1";
+system($cmd5);
+
+my $cmd='';
+if (($R eq 'tss')||($R eq 'tes')) {
+   $cmd = "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 >> $logfile 2>&1";
+}elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_region_size') {
+   if ($IN eq 'automatic') {
+      $cmd = "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";
+   }else {
+      $cmd = "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  >> $logfile 2>&1";
+   }
+}elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_floating_size') {
+   if ($IN eq 'automatic') {
+      $cmd = "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";
+   }else {
+      $cmd = "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";
+   }
+}
+my $cmd2="cp data.zip $O";
+my $cmd3="rm $outfile";
+my $cmd4="rm $logfile";
+syswrite(FILE2, "\n$cmd\n");
+syswrite(FILE2, "\n$cmd2\n");
+syswrite(FILE2, "\n$cmd3\n");
+syswrite(FILE2, "\n$cmd4\n\n");
+
+system($cmd);
+system($cmd2);
+system($cmd3);
+system($cmd4);
+
+close(FILE2);
+
+