--- a/augustus.xml	Sat Jul 06 10:07:41 2013 -0400
+++ b/augustus.xml	Thu Dec 05 09:44:17 2013 -0500
@@ -1,5 +1,6 @@
-<tool id="augustus" name="Augustus" version="0.3">
+<tool id="augustus" name="Augustus" version="0.3.1">
     <description>gene prediction for eukaryotic genomes</description>
+    <parallelism method="multi" split_inputs="input_genome" split_mode="to_size" split_size="10" merge_outputs="output,protein_output,codingseq_output"></parallelism>
     <requirements>
         <requirement type="package" version="2.7">augustus</requirement>
         <requirement type="set_environment">AUGUSTUS_SCRIPT_PATH</requirement>
@@ -13,12 +14,43 @@
             --strand=$strand
             $noInFrameStop
             $gff
-            $protein
-            $introns
-            $start
-            $stop
-            $cds
-            $codingseq
+            
+            #if 'protein' in str($outputs).split(','):
+                --protein=on
+            #else:
+                --protein=off
+            #end if
+
+            #if 'codingseq' in str($outputs).split(','):
+                --codingseq=on
+            #else:
+                --codingseq=off
+            #end if
+            
+            #if 'introns' in str($outputs).split(','):
+                --introns=on
+            #else:
+                --introns=off
+            #end if
+
+            #if 'start' in str($outputs).split(','):
+                --start=on
+            #else:
+                --stop=off
+            #end if
+
+            #if 'stop' in str($outputs).split(','):
+                --stop=on
+            #else:
+                --stop=off
+            #end if
+
+            #if 'cds' in str($outputs).split(','):
+                --cds=on
+            #else:
+                --cds=off
+            #end if
+
             $singlestrand
             $input_genome
             $mea
@@ -27,12 +59,12 @@
             --species=$organism
             ##--outfile=$output
         | tee $output 
-        #if $protein or $codingseq:
+        #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
             | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py
-                #if $protein:
+                #if 'protein' in str($outputs).split(','):
                     --protein $protein_output
                 #end if
-                #if $codingseq:
+                #if 'codingseq' in str($outputs).split(','):
                     --codingseq $codingseq_output
                 #end if
         #end if
@@ -121,14 +153,21 @@
             <option value="bacterium">bacterium (beta version)</option>
         </param>
 
-        <param name="protein" type="boolean" label="Output predicted protein sequences (--protein)" truevalue="--protein=on" falsevalue="--protein=off" checked="true" />
-        <param name="codingseq" type="boolean" label="Output coding sequence as comment in the output file (codingseq)" truevalue="--codingseq=on" falsevalue="--codingseq=off" checked="true" />
-        <param name="introns" type="boolean" label="Output predicted intron sequences (--introns)" truevalue="--introns=on" falsevalue="--introns=off" checked="false" />
-        <param name="start" type="boolean" label="Output predicted start codons (--start)" truevalue="--start=on" falsevalue="--start=off" checked="false" />
-        <param name="stop" type="boolean" label="Output predicted stop codons (--stop)" truevalue="--stop=on" falsevalue="--stop=off" checked="false" />
-        <param name="cds" type="boolean" label="Output CDS region (--cds)" truevalue="--cds=on" falsevalue="--cds=off" checked="true" />
+
         <param name="gff" type="boolean" label="GFF formated output, standard is GTF (--gff3)" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
 
+        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
+            <option value="protein" selected="True">predicted protein sequences (--protein)</option>
+            <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option>
+            <option value="introns">predicted intron sequences (--introns)</option>
+            <option value="start">predicted start codons (--start)</option>
+            <option value="stop">predicted stop codons (--stop)</option>
+            <option value="cds" selected="true">CDS region (--cds)</option>
+
+            <validator type="no_options" message="Please select at least one output file." />
+        </param>
+
+
     </inputs>
     <outputs>
         <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
@@ -137,10 +176,10 @@
             </change_format>
         </data>
         <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
-            <filter>protein == True</filter>
+            <filter>'protein' in outputs</filter>
         </data>
         <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
-            <filter>codingseq == True</filter>
+            <filter>'codingseq' in outputs</filter>
         </data>
     </outputs>
     <tests>
@@ -167,10 +206,7 @@
         <test>
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
-            <param name="protein" value="--protein=on" />
-            <param name="codingseq" value="--codingseq=on" />
-            <param name="introns" value="--introns=on" />
-            <param name="cds" value="--cds=on" />
+            <param name="outputs" value="protein,codingseq,introns,cds" />
             <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" lines_diff="2"/>
             <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
             <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />