--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glang-galaxy-conf/kbws/acdgalaxy.pl	Fri Jun 26 05:21:44 2015 -0400
@@ -0,0 +1,194 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+
+my $progname = shift;
+$progname =~ s/\.acd$//g;
+my $progfile = "/usr/local/share/EMBOSS/acd/$progname.acd";
+open my $acdfh, "<", $progfile;
+open my $xmlfh, ">", "$progname.xml";
+
+my $tool;
+my $description;
+my $command;
+my @params;
+my @args;
+my $help;
+my $plot = 0+`grep -c 'toggle: plot' $progfile`;
+my $pngout = 0+`grep -c 'string: format' $progfile`;
+
+while(<$acdfh>) {
+    chomp;
+    if(/\s*application\s*:\s*\w+\s*\[\s*$/../^\s*\]\s*$/) {
+        if(/\s*application\s*:\s*(\w+)\s*\[\s*$/) {
+            $tool = qq(<tool id="EMBOSS: $1" name="$1" version="1.0.2">);
+        }
+
+        if(/\s*documentation:\s*"([^"]+)"?\s*/) {
+            my $tmp = $1;
+            if(/\s*documentation:\s*".+"\s*/) {
+                $description = qq(  <description>$tmp</description>);
+            } else {
+                while(<$acdfh>) {
+                    if(/\s*(.*)"/) {
+                        $tmp.= " $1";
+                        last;
+                    } elsif(/\s*(.*)\s*/) {
+                        $tmp .= " $1";
+                    }
+                }
+                $description = qq(  <description>$tmp</description>);
+            }
+        }
+    }
+
+    if(/\s*section\s*:\s*advanced\s*\[/../\s*endsection:\s*advanced/) {
+        if(/\s*section\s*:\s*advanced\s*\[/../\]/ or /\s*endsction:\s*advanced/) {
+            next;
+        }
+
+        if(/\s*\w+\s*:\s*\w+\s*\[/../\s*\]/) {
+            if(/\s*(\w+)\s*:\s*(\w+)\s*\[/) {
+                my ($type, $name) = ($1, $2);
+                my $information;
+                my $default;
+                my @values;
+
+                next if $name eq "accid";
+                next if $name eq "plot";
+
+                push @args, $name;
+
+                while(<$acdfh>) {
+                    chomp;
+                    if(/\]/) {
+                        last;
+                    }
+                    if(/\s*information:\s*"([^"]+)"?\s*/) {
+                        my $tmp = $1;
+                        if(/\s*information:\s*".+"\s*/) {
+                            $information = $tmp;
+                        } else {
+                            while(<$acdfh>) {
+                                if(/\s*(.*)"/) {
+                                    $tmp.= " $1";
+                                    last;
+                                } elsif(/\s*(.*)\s*/) {
+                                    $tmp .= " $1";
+                                }
+                            }
+                            $information = $tmp;
+                        }
+                    }
+
+                    if(/\s*default:\s*"(.+)"\s*/) {
+                        $default = $1;
+                    }
+
+                    if(/\s*values:\s*"(.+)"\s*/) {
+                        @values = split ";", $1;
+                    }
+                }
+                #print "$type\t$name\t$information";
+                #print "\t$default" if defined $default;
+                #print "\n";
+                my $param;
+
+                if($default) {
+                    $default = "yes" if $default eq "Y";
+                    $default = "no"  if $default eq "N";
+                    $default = "[^ACDEFGHIKLMNPQRSTVWYacgtU]" if $name eq "delkey";
+                } else {
+                    $default = "";
+                }
+
+                if($type eq "boolean") {
+                    $param = <<EOS;
+    <param name="$name" type="select" value="$default">
+      <label>$information</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+EOS
+                }
+
+                if($type =~ /(integer)|(float)|(string)/) {
+                    $type =~ s/string/text/g;
+                    $param = <<EOS;
+    <param name="$name" size="4" type="$type" value="$default">
+      <label>$information</label>
+    </param>
+EOS
+                }
+
+                if($type =~ /selection/) {
+                    my $vals = join "\n", map{
+                        "      <option value=\"$_\">". ucfirst($_) ."</option>"
+                    }@values;
+                    $param = <<EOS
+    <param name="$name" type="select" value="$default">
+      <label>$information</label>
+$vals
+    </param>
+EOS
+                }
+
+                print "$type: $name\n";
+                if($param && length $param) {
+                    chomp($param);
+                    push @params, $param;
+                }
+            }
+        }
+    }
+}
+close $acdfh;
+
+my $args = join(" ", map{"-$_ \$$_"}@args);
+
+my $paramstr = "";
+foreach my $param (@params) {
+    $paramstr .= "$param\n";
+}
+
+my $outputs;
+
+if($plot) {
+    $command = "<command interpreter=\"perl\">gembassy_calcandplot_wrapper.pl $progname -sequence \$input1 $args -auto \$out_file1 \$out_file2</command>";
+    $outputs = <<EOS;
+    <data format="csv" name="out_file1" label="\${tool.name} data for \${input1.name}" />
+    <data format="png" name="out_file2" label="\${tool.name} plot for \${input1.name}" />
+EOS
+} elsif($pngout) {
+    $command = "<command interpreter=\"perl\">emboss_single_outputfile_wrapper.pl $progname -sequence \$input1 -format png -goutfile \$out_file1 -auto $args</command>";
+    $outputs = <<EOS;
+    <data format="png" name="out_file1" label="\${tool.name} for \${input1.name}" />
+EOS
+} else {
+    $command = "<command>$progname -sequence \$input1 $args -auto -outfile \$out_file1</command>";
+    printf(STDERR "Enter output data format of $progname (1: txt 2: csv): ");
+    chomp(my $format = <>);
+    $format = $format == 1 ? "txt" : "csv";
+    $outputs = <<EOS;
+    <data format="$format" name="out_file1" label="\${tool.name} for \${input1.name}" />
+EOS
+}
+chomp $outputs;
+
+print $xmlfh <<EOS;
+$tool
+$description
+  $command
+  <inputs>
+  <param format="data" name="input1" type="data">
+    <label>Sequence</label>
+  </param>
+$paramstr
+  </inputs>
+  <outputs>
+$outputs    
+  </outputs>
+</tool>
+EOS
+
+close $xmlfh;