--- 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" />

--- a/readme.rst	Sat Jul 06 10:07:41 2013 -0400
+++ b/readme.rst	Thu Dec 05 09:44:17 2013 -0500
@@ -28,7 +28,7 @@
 The recommended installation is by means of the toolshed_.
 If you need to install it manually here is a short introduction.
 
-.. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/augustus
+.. _toolshed:  http://toolshed.g2.bx.psu.edu/view/bgruening/augustus
 
 
 Install or downlaod augustus from::
@@ -59,25 +59,26 @@
 - v0.1: Initial public release
 - v0.2: Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
 - v0.3: upgrade to augustus 2.7, added new organisms and new parameters, output additional sequence files
+- v0.3.1: added parallelism and changed the output parameters from boolean to a select box
 
-Wrapper Licence (MIT/BSD style)
-===============================
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
 
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.