Mercurial > repos > ngsplot > ngsplot
diff ngsplot_galaxytoolshed/ngsplot_replot/runreplot.pl @ 0:e6028c2c3da3 draft
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author | ngsplot |
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date | Wed, 18 Mar 2015 14:08:10 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ngsplot_galaxytoolshed/ngsplot_replot/runreplot.pl Wed Mar 18 14:08:10 2015 -0400 @@ -0,0 +1,63 @@ +#!/usr/bin/perl -w +use strict; +use File::Basename 'dirname'; +use File::Spec; +use Cwd 'abs_path'; + +my $input_file = $ARGV[0]; +my $output_type = $ARGV[1]; +my $output_filename = $ARGV[2]; + +my $cmd1 = "cp $input_file data.zip"; +my $cmd2 = ""; +my $cmd3 = "mv output.pdf $output_filename"; + +my $FS = ""; +if ($output_type eq 'prof') { + my $WD = "-WD $ARGV[3]"; + my $HG = "-HG $ARGV[4]"; + my $SE = "-SE $ARGV[5]"; + my $H = "-H $ARGV[6]"; + my $MW = "-MW $ARGV[7]"; + my $Y = "-Y $ARGV[8]"; + my $YAS = "-YAS $ARGV[9]"; + my $LEG = "-LEG $ARGV[10]"; + my $BOX = "-BOX $ARGV[11]"; + my $VLN = "-VLN $ARGV[12]"; + my $XYL = "-XYL $ARGV[13]"; + my $LWD = "-LWD $ARGV[14]"; + $FS = "-FS $ARGV[15]"; + + if ($Y =~ /no$/gm) { + $cmd2 = "replot.r $output_type -I data.zip -O output $WD $HG $SE $H $MW $LEG $BOX $VLN $XYL $LWD $FS"; + }else { + $cmd2 = "replot.r $output_type -I data.zip -O output $WD $HG $SE $H $MW $LEG $BOX $VLN $XYL $LWD $FS $YAS"; + } +}elsif ($output_type eq 'heatmap') { + my $GO = "-GO $ARGV[3]"; + my $KNC = "-KNC $ARGV[4]"; + my $MIT = "-MIT $ARGV[5]"; + my $NRS = "-NRS $ARGV[6]"; + my $LOW = "-LOW $ARGV[7]"; + my $RR = "-RR $ARGV[8]"; + my $FC = "-FC $ARGV[9]"; + my $CO = "-CO $ARGV[10]"; + my $CD = "-CD $ARGV[11]"; + $FS = "-FS $ARGV[12]"; + my $DUM1 = $ARGV[13]; + my $DUM2 = $ARGV[14]; + my $DUM3 = $ARGV[15]; + + if ($CO =~ /default/gm) { $CO = ""; } + + if ($GO =~ /km$/gm) { + $cmd2 = "replot.r $output_type -I data.zip -O output $LOW $RR $FC $CO $CD $FS $GO $KNC $MIT $NRS"; + }else { + $cmd2 = "replot.r $output_type -I data.zip -O output $LOW $RR $FC $CO $CD $FS $GO"; + } +} +system($cmd1); +system($cmd2); +system($cmd3); + +