--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chewBBACA.pl	Fri May 03 10:06:09 2019 -0400
@@ -0,0 +1,149 @@
+#!/usr/bin/env perl
+## A wrapper script to call chewBBACA.py and collect its output
+use strict;
+use warnings;
+use Cwd;
+use English;
+use File::Copy;
+use File::Basename;
+
+# Parse arguments
+my ($myFunction,
+    $input1,
+    $input1_names,
+    $output,
+    $python) = @ARGV;
+
+# Run program
+my $abs_path = Cwd::abs_path($PROGRAM_NAME);
+my $scriptdir = dirname($abs_path);
+
+prepareEnvironment($input1,$input1_names,"input_dir");
+runChewBBACA();
+collectOutput();
+exit(0);
+
+# Run chewBBACA
+sub runChewBBACA {
+    my $abs_path = Cwd::abs_path($PROGRAM_NAME);
+    my $scriptdir = dirname($abs_path);
+    my $createschemadir = "$scriptdir/createschema";
+    my $allelecalldir = "$scriptdir/allelecall";
+    my $SchemaEvaluatordir = "$scriptdir/SchemaEvaluator";
+    my $utilsdir = "$scriptdir/utils";
+    my $newpath = "PATH=$ENV{PATH}:$createschemadir:$allelecalldir:$SchemaEvaluatordir:$utilsdir";
+    my $result = system("$newpath; $python");
+    return 0;
+}
+
+# Run prepareEnvironment, create the directory $indir with symlinks to the files listed in $inlist
+sub prepareEnvironment {
+    my ($inlist, $inlist_names, $indir) = @_;
+    if ($inlist ne "NULL") {
+      mkdir($indir);
+      my @inputs = split(',', $inlist);
+      if ($inlist_names ne "NULL") {
+        my @inputs_names = split(',', $inlist_names);
+        for my $i ( 0 .. $#inputs ){
+          my $name = $inputs_names[$i];
+          $name =~ s/ /_/g;
+          $name =~ s/\//_/g;
+          $name =~ s/\(/_/g;
+          $name =~ s/\)/_/g;
+          $name =~ s/\[/_/g;
+          $name =~ s/\]/_/g;
+          $name =~ s/\{/_/g;
+          $name =~ s/\}/_/g;
+          symlink($inputs[$i], $indir . "/" . $name);
+        }
+      }
+      else {
+        foreach my $i (@inputs){
+          symlink($i, $indir . "/" . basename($i));
+        }
+      }
+    }
+    return 0;
+}
+
+# Collect output
+sub collectOutput{
+    # CreateSchema
+    if ($myFunction eq "CreateSchema") {
+      my($dataname, $datadir, $datasuffix) = fileparse($output,qr/\.[^.]*/);
+      my @fasta_files = glob "output_dir/*.fasta";
+      my $dest_dir = $datadir . $dataname . "/";
+      mkdir($dest_dir);
+      open(my $fh1, '>', $output) or die "Could not open file '$output' $!";
+      my $new_fasta_file = "";
+      foreach my $fasta_file (@fasta_files) {
+         $new_fasta_file = $dest_dir . basename($fasta_file);
+         print $fh1 "$new_fasta_file\n";
+         move($fasta_file, $new_fasta_file) or die "Could not move $fasta_file: $!\n";
+      }
+      close $fh1;
+      my @short_fasta_files = glob "output_dir/short/*.fasta";
+      my $short_dest_dir = $datadir . $dataname . "/short/";
+      mkdir($short_dest_dir);
+      foreach my $short_fasta_file (@short_fasta_files) {
+         move($short_fasta_file, $short_dest_dir) or die "Could not move $short_fasta_file: $!\n";
+      }
+    }
+    # AlleleCall
+    if ($myFunction eq "AlleleCall") {
+      my @outputs = split(',', $output);
+      my @statistics = glob "output_dir/results_*/results_statistics.tsv";
+      if (@statistics == 1) {
+        move($statistics[0], $outputs[0])
+      }
+      my @contigsinfo = glob "output_dir/results_*/results_contigsInfo.tsv";
+      if (@contigsinfo == 1) {
+        move($contigsinfo[0], $outputs[1])
+      }
+      my @alleles = glob "output_dir/results_*/results_alleles.tsv";
+      if (@alleles == 1) {
+        move($alleles[0], $outputs[2])
+      }
+      my @logginginfo = glob "output_dir/results_*/logging_info.txt";
+      if (@logginginfo == 1) {
+        move($logginginfo[0], $outputs[3])
+      }
+      my @repeatedloci = glob "output_dir/results_*/RepeatedLoci.txt";
+      if (@repeatedloci == 1) {
+        move($repeatedloci[0], $outputs[4])
+      }
+    }
+    # SchemaEvaluator
+    if ($myFunction eq "SchemaEvaluator") {
+      my($dataname, $datadir, $datasuffix) = fileparse($output,qr/\.[^.]*/);
+      my @output_files = glob "output_rms/*.*";
+      my $dest_dir = $dataname . "/";
+      mkdir($dest_dir);
+      my $new_output_file = "";
+      foreach my $output_file (@output_files) {
+         $new_output_file = $dest_dir . basename($output_file);
+         move($output_file, $new_output_file) or die "Could not move $output_file: $!\n";
+      }
+      open(my $fh2, '<', $dest_dir . "SchemaEvaluator.html") || die "File not found";
+      my @lines = <$fh2>;
+      close($fh2);
+      my @newlines;
+      foreach(@lines) {
+         $_ =~ s/\.\.\/\.\.\/\.\.\/.*?\/database\/files\/...\/dataset/dataset/g;
+         push(@newlines,$_);
+      }
+      # write the html to the Galaxy output file
+      #open($fh2, '>', $output) || die "File not found";
+      #print $fh2 @newlines;
+      #close($fh2);
+      my @html_output_files = glob "output_rms/genes_html/*.*";
+      my $html_dest_dir = $dest_dir . "genes_html/";
+      mkdir($html_dest_dir);
+      foreach my $html_output_file (@html_output_files) {
+         move($html_output_file, $html_dest_dir) or die "Could not move $html_output_file: $!\n";
+      }
+      my $cmd = `tar -cpf $output $dest_dir`;
+    }
+    return 0;
+}
+