--- a/augustus.xml	Fri Jun 07 02:30:21 2013 -0400
+++ b/augustus.xml	Sun Jun 09 09:53:26 2013 -0400
@@ -2,7 +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>
+        <requirement type="set_environment">AUGUSTUS_SCRIPT_PATH</requirement>
     </requirements>
     <command>
         ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
@@ -28,7 +28,7 @@
             ##--outfile=$output
         | tee $output 
         #if $protein or $codingseq:
-            | python \$SCRIPT_PATH/extract_features.py
+            | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py
                 #if $protein:
                     --protein $protein_output
                 #end if
@@ -148,21 +148,21 @@
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
             <param name="utr" value="--UTR=on" />
-            <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" />
+            <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <test>
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
             <param name="utr" value="--UTR=on" />
             <param name="gff" value="--gff3=on" />
-            <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" />
+            <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="2"/>
         </test>
         <test>
             <param name="input_genome" value="arabidopsis_augustus.fa" ftype="fasta" />
             <param name="organism" value="arabidopsis" />
             <param name="singlestrand" value="--singlestrand=true" />
             <param name="mea" value="--mea=1" />
-            <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" />
+            <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/>
         </test>
         <test>
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
@@ -171,7 +171,7 @@
             <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="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" />
         </test>