# HG changeset patch
# User bgruening
# Date 1370786006 14400
# Node ID bcfe8e0731f8b622dd97c1acf62e0922de3362a8
# Parent  c243e17fb224e03053cf4475358f39e711702f35
Uploaded

diff -r c243e17fb224 -r bcfe8e0731f8 augustus.xml
--- 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>
diff -r c243e17fb224 -r bcfe8e0731f8 extract_features.py
--- a/extract_features.py	Fri Jun 07 02:30:21 2013 -0400
+++ b/extract_features.py	Sun Jun 09 09:53:26 2013 -0400
@@ -47,16 +47,18 @@
 
             if args.protein and line.startswith('protein sequence = ['):
                 if line.endswith(']'):
-                    line = line[20:-1]
-                    protein_seq = line
+                    protein_seq = line[20:-1]
+                    po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
+                    protein_seq = ''
                 else:
                     line = line[20:]
                     protein_seq = line
 
             if args.codingseq and line.startswith('coding sequence = ['):
                 if line.endswith(']'):
-                    line = line[19:-1]
-                    coding_seq = line
+                    coding_seq = line[19:-1]
+                    co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
+                    coding_seq = ''
                 else:
                     line = line[19:]
                     coding_seq = line
diff -r c243e17fb224 -r bcfe8e0731f8 readme.rst
--- a/readme.rst	Fri Jun 07 02:30:21 2013 -0400
+++ b/readme.rst	Sun Jun 09 09:53:26 2013 -0400
@@ -3,8 +3,9 @@
 
 This wrapper is copyright 2012-2013 by Björn Grüning.
 
-This is a wrapper for the command line tool of augustus.
-http://bioinf.uni-greifswald.de/augustus/
+This is a wrapper for the command line tool of Augustus_.
+
+.. _augustus: http://bioinf.uni-greifswald.de/augustus/
 
 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
 
@@ -24,10 +25,15 @@
 Installation
 ============
 
-The recommended installation is by means of the tool shed. If you need to install it manually here is a short introduction.
+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
 
-Install or downlaod augustus from:
-http://bioinf.uni-greifswald.de/augustus/binaries/
+
+Install or downlaod augustus from::
+
+    http://bioinf.uni-greifswald.de/augustus/binaries/
 
 and follow the installation instructions or copy the binaries into your $PATH. To install the wrapper copy the augustus folder in the galaxy tools folder and modify the tools_conf.xml file to make the tool available to Galaxy.
 
diff -r c243e17fb224 -r bcfe8e0731f8 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jun 07 02:30:21 2013 -0400
+++ b/tool_dependencies.xml	Sun Jun 09 09:53:26 2013 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <set_environment version="1.0">
-        <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+        <environment_variable name="AUGUSTUS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
     <package name="augustus" version="2.7">
         <install version="1.0">