--- a/augustus.xml	Thu Jun 06 12:51:27 2013 -0400
+++ b/augustus.xml	Thu Jun 06 13:26:37 2013 -0400
@@ -2,6 +2,7 @@
     <description>gene prediction for eukaryotic genomes</description>
     <requirements>
         <requirement type="package" version="2.7">augustus</requirement>
+        <requirement type="set_environment">SCRIPT_PATH</requirement>
     </requirements>
     <command>
         ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
@@ -27,7 +28,7 @@
             ##--outfile=$output
         | tee $output 
         #if $protein or $codingseq:
-            | python extract_features.py 
+            | python \$SCRIPT_PATH/extract_features.py
                 #if $protein:
                     --protein $protein_output
                 #end if
@@ -136,10 +137,10 @@
             </change_format>
         </data>
         <data format="fasta" name="protein_output">
-            <filter>protein == "--protein=on"</filter>
+            <filter>protein == True</filter>
         </data>
         <data format="fasta" name="codingseq_output">
-            <filter>codingseq == "--codingseq=on"</filter>
+            <filter>codingseq == True</filter>
         </data>
     </outputs>
     <tests>
@@ -163,6 +164,17 @@
             <param name="mea" value="--mea=1" />
             <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on" ftype="gtf" />
         </test>
+        <test>
+            <param name="input_genome" value="HS04636_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" />
+            <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" />
+            <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" />
+        </test>
     </tests>
     <help>