comparison runNGSplot.pl @ 3:de27d4172d19 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'60a55d19937d9dc976020e1c396948b41967a7f8\n'

2:4b4d858c0aa9

   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");
   }

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 $cmd5="pwd >> $logfile 2>&1";
system($cmd5);
my $NGSPLOT = $ENV{"NGSPLOT"};
my $cmd='';
if (($R eq 'tss')||($R eq 'tes')) {
   $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 >> $logfile 2>&1";
}elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_region_size') {
   if ($IN eq 'automatic') {
      $cmd = "$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";
   }else {
      $cmd = "$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  >> $logfile 2>&1";
   }
}elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_floating_size') {
   if ($IN eq 'automatic') {
      $cmd = "$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";
   }else {
      $cmd = "$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";
   }
}

print("$cmd\n");
my $cmd2="cp data.zip $O";
my $cmd3="rm $outfile";
syswrite(FILE2, "\n$cmd\n");
syswrite(FILE2, "\n$cmd2\n");
syswrite(FILE2, "\n$cmd3\n");

# print STDERR "cmd: $cmd\n";
system($cmd);
system($cmd2);
system($cmd3);

close(FILE2);

3:de27d4172d19

   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");
   }

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 $cmd5="pwd >> $logfile 2>&1";
system($cmd5);
my $NGSPLOT = $ENV{"NGSPLOT"};
my $cmd='';
if (($R eq 'tss')||($R eq 'tes')) {
   $cmd = "Rscript $NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -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') {
      $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -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 {
      $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -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') {
      $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -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 {
      $cmd = "$NGSPLOT/ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -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";
   }
}

print("$cmd\n");
#my $cmd2="cp data.zip $O";
#my $cmd3="rm $outfile";
syswrite(FILE2, "\n$cmd\n");
#syswrite(FILE2, "\n$cmd2\n");
#syswrite(FILE2, "\n$cmd3\n");

# print STDERR "cmd: $cmd\n";
system($cmd);
#system($cmd2);
#system($cmd3);

close(FILE2);