diff runreplot.pl @ 0:3ca58369469c draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runreplot.pl	Wed Dec 06 19:01:53 2017 -0500
@@ -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);
+
+