# HG changeset patch
# User Bjoern Gruening <bjoern@gruenings.eu>
# Date 1331802568 -3600
# Node ID d5d5999ff4f1e3ffe934ddcccd0c92bc5dc18298
# Parent  5663d1a1b29c0e25ea17754fff964dd674a500a5
change directory structure

diff -r 5663d1a1b29c -r d5d5999ff4f1 augustus.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/augustus.xml	Thu Mar 15 10:09:28 2012 +0100
@@ -0,0 +1,186 @@
+<tool id="augustus" name="Augustus" version="0.1">
+	<description>gen prediction for eukaryotic genomes</description>
+    <command>augustus
+        --strand=$strand
+        $noInFrameStop
+        $gff
+        $protein
+        $introns
+        $start
+        $stop
+        $cds
+        $codingseq
+        $singlestrand
+        $input_genome 
+        --genemodel=$genemodel
+        --species=$organism
+        --outfile=$output
+
+        #please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+        #or use the --AUGUSTUS_CONFIG_PATH=path switch
+
+    </command>
+	<inputs>
+		<param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
+		<param name="noInFrameStop" type="boolean" label="Don't report transcripts with in-frame stop codons. Otherwise, intron-spanning stop codons could occur" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" />
+		<param name="gff" type="boolean" label="GFF formated output, standard is GTF" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
+		<param name="protein" type="boolean" label="Output predicted protein sequences" truevalue="--protein=on" falsevalue="--protein=off" checked="false" />
+		<param name="introns" type="boolean" label="Output predicted intron sequences" truevalue="--introns=on" falsevalue="--introns=off" checked="false" />
+		<param name="start" type="boolean" label="Output predicted start codons" truevalue="--start=on" falsevalue="--start=off" checked="false" />
+		<param name="stop" type="boolean" label="Output predicted stop codons" truevalue="--stop=on" falsevalue="--stop=off" checked="false" />
+		<param name="cds" type="boolean" label="Output CDS region" truevalue="--cds=on" falsevalue="--cds=off" checked="true" />
+		<param name="codingseq" type="boolean" label="Output coding sequence as comment in the output file" truevalue="--codingseq=on" falsevalue="--codingseq=off" checked="false" />
+
+		<param name="singlestrand" type="boolean" label="Predict genes independently on each strand, allow overlapping genes on opposite strands" truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
+
+        <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
+            <option value="human">Homo sapiens</option>
+            <option value="fly">Drosophila melanogaster</option>
+            <option value="arabidopsis">Arabidopsis thaliana</option>
+            <option value="brugia ">Brugia malayi</option>
+            <option value="aedes">Aedes aegypti</option>
+            <option value="tribolium">Tribolium castaneum</option>
+            <option value="schistosoma">Schistosoma mansoni</option>
+            <option value="tetrahymena">Tetrahymena thermophila</option>
+            <option value="galdieria">Galdieria sulphuraria</option>
+            <option value="maize">Zea mays</option>
+            <option value="toxoplasma ">Toxoplasma gondii</option>
+            <option value="caenorhabditis ">Caenorhabditis elegans</option>
+            <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
+            <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
+            <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
+            <option value="aspergillus_terreus">Aspergillus terreus</option>
+            <option value="botrytis_cinerea ">Botrytis cinerea</option>
+            <option value="candida_albicans ">Candida albicans</option>
+            <option value="candida_guilliermondii ">Candida guilliermondii</option>
+            <option value="candida_tropicalis ">Candida tropicalis</option>
+            <option value="chaetomium_globosum">Chaetomium globosum</option>
+            <option value="coccidioides_immitis ">Coccidioides immitis</option>
+            <option value="coprinus ">Coprinus cinereus</option>
+            <option value="coprinus_cinereus">Coprinus cinereus</option>
+            <option value="cryptococcus_neoformans_gattii ">Cryptococcus neoformans gattii</option>
+            <option value="cryptococcus_neoformans_neoformans_B ">Cryptococcus neoformans neoformans</option>
+            <option value="cryptococcus_neoformans_neoformans_JEC21 ">Cryptococcus neoformans neoformans</option>
+            <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
+            <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
+            <option value="eremothecium_gossypii">Eremothecium gossypii</option>
+            <option value="fusarium_graminearum ">Fusarium graminearum</option>
+            <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
+            <option value="(histoplasma)">Histoplasma capsulatum</option>
+            <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
+            <option value="laccaria_bicolor ">Laccaria bicolor</option>
+            <option value="lamprey">Petromyzon marinus</option>
+            <option value="leishmania_tarentolae">Leishmania tarentolae</option>
+            <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
+            <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
+            <option value="neurospora_crassa">Neurospora crassa</option>
+            <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
+            <option value="pichia_stipitis">Pichia stipitis</option>
+            <option value="rhizopus_oryzae">Rhizopus oryzae</option>
+            <option value="saccharomyces_cerevisiae_S288C ">Saccharomyces cerevisiae</option>
+            <option value="saccharomyces_cerevisiae_rm11-1a_1 ">Saccharomyces cerevisiae</option>
+            <option value="(saccharomyces)">Saccharomyces cerevisiae</option>
+            <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
+            <option value="trichinella">Trichinella spiralis</option>
+            <option value="ustilago_maydis">Ustilago maydis</option>
+            <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
+            <option value="nasonia">Nasonia vitripennis</option>
+            <option value="tomato ">Solanum lycopersicum</option>
+            <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
+            <option value="amphimedon ">Amphimedon queenslandica</option>
+            <option value="pneumocystis ">Pneumocystis jirovecii</option>
+        </param> 
+
+        <param name="strand" type="select" multiple="false" format="text" help="Report predicted genes on both strands, just the forward or just the backward strand.">
+            <option value="both">both</option>
+            <option value="forward">forward</option>
+            <option value="backward">backward</option>
+        </param> 
+
+        <param name="genemodel" label="Gene Model" type="select" multiple="false" format="text" help="Gene Model to predict, for more information please refere to the help.">
+            <option value="complete">complete</option>
+            <option value="partial">partial</option>
+            <option value="intronless">intronless</option>
+            <option value="atleastone">atleastone</option>
+            <option value="exactlyone">exactlyone</option>
+        </param>
+
+	</inputs>
+	<outputs>
+        <data format="gtf" name="output">
+            <change_format>
+                <when input="gff" value="--gff3=on" format="gff" />
+            </change_format>
+        </data>
+    </outputs>
+    <requirements>
+        <requirement type="binary">augustus</requirement>
+    </requirements>
+    <help>
+
+**What it does**
+
+AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
+It can be used as an ab initio program, which means it bases its prediction purely on the
+sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
+such as EST, MS/MS, protein alignments and synthenic genomic alignments.
+
+-----	
+
+**Parameters**
+
+Gene Model::
+
+    partial      : allow prediction of incomplete genes at the sequence boundaries (default)
+    intronless   : only predict single-exon genes like in prokaryotes and some eukaryotes
+    complete     : only predict complete genes
+    atleastone   : predict at least one complete gene
+    exactlyone   : predict exactly one complete gene
+
+
+
+**Example**
+
+Suppose you have the following DNA formatted sequences::
+
+    >Seq1
+    cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
+    ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
+    cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
+    cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
+    ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
+
+Running this tool will produce this::
+
+    # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----
+    #
+    # Constraints/Hints:
+    # (none)
+    # Predicted genes for sequence number 1 on both strands
+    # start gene g1
+    scaffold1|size1992969	AUGUSTUS	gene	17453	19382	0.11	+	.	g6
+    scaffold1|size1992969	AUGUSTUS	transcript	17453	19382	0.11	+	.	g6.t1
+    scaffold1|size1992969	AUGUSTUS	start_codon	17453	17455	.	+	0	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	intron	17615	17660	0.38	+	.	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	intron	17708	17772	0.54	+	.	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	intron	17902	18035	0.58	+	.	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	intron	18313	18367	0.99	+	.	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	intron	19014	19080	0.44	+	.	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	CDS	17453	17614	0.55	+	0	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	CDS	17661	17707	0.38	+	0	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	CDS	17773	17901	0.54	+	1	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	CDS	18036	18312	0.52	+	1	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	CDS	18368	19013	0.99	+	0	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	CDS	19081	19379	0.31	+	2	transcript_id "g6.t1"; gene_id "g6";
+    scaffold1|size1992969	AUGUSTUS	stop_codon	19380	19382	.	+	0	transcript_id "g6.t1"; gene_id "g6";
+
+
+**References**
+
+Mario Stanke and Stephan Waack (2003) 
+Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. 
+Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
+
+
+	</help>
+</tool>
diff -r 5663d1a1b29c -r d5d5999ff4f1 augustus/augustus.xml
--- a/augustus/augustus.xml	Wed Mar 14 17:07:11 2012 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,186 +0,0 @@
-<tool id="augustus" name="Augustus" version="0.1">
-	<description>gen prediction for eukaryotic genomes</description>
-    <command>augustus
-        --strand=$strand
-        $noInFrameStop
-        $gff
-        $protein
-        $introns
-        $start
-        $stop
-        $cds
-        $codingseq
-        $singlestrand
-        $input_genome 
-        --genemodel=$genemodel
-        --species=$organism
-        --outfile=$output
-
-        #please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
-        #or use the --AUGUSTUS_CONFIG_PATH=path switch
-
-    </command>
-	<inputs>
-		<param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
-		<param name="noInFrameStop" type="boolean" label="Don't report transcripts with in-frame stop codons. Otherwise, intron-spanning stop codons could occur" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" />
-		<param name="gff" type="boolean" label="GFF formated output, standard is GTF" truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
-		<param name="protein" type="boolean" label="Output predicted protein sequences" truevalue="--protein=on" falsevalue="--protein=off" checked="false" />
-		<param name="introns" type="boolean" label="Output predicted intron sequences" truevalue="--introns=on" falsevalue="--introns=off" checked="false" />
-		<param name="start" type="boolean" label="Output predicted start codons" truevalue="--start=on" falsevalue="--start=off" checked="false" />
-		<param name="stop" type="boolean" label="Output predicted stop codons" truevalue="--stop=on" falsevalue="--stop=off" checked="false" />
-		<param name="cds" type="boolean" label="Output CDS region" truevalue="--cds=on" falsevalue="--cds=off" checked="true" />
-		<param name="codingseq" type="boolean" label="Output coding sequence as comment in the output file" truevalue="--codingseq=on" falsevalue="--codingseq=off" checked="false" />
-
-		<param name="singlestrand" type="boolean" label="Predict genes independently on each strand, allow overlapping genes on opposite strands" truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />
-
-        <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
-            <option value="human">Homo sapiens</option>
-            <option value="fly">Drosophila melanogaster</option>
-            <option value="arabidopsis">Arabidopsis thaliana</option>
-            <option value="brugia ">Brugia malayi</option>
-            <option value="aedes">Aedes aegypti</option>
-            <option value="tribolium">Tribolium castaneum</option>
-            <option value="schistosoma">Schistosoma mansoni</option>
-            <option value="tetrahymena">Tetrahymena thermophila</option>
-            <option value="galdieria">Galdieria sulphuraria</option>
-            <option value="maize">Zea mays</option>
-            <option value="toxoplasma ">Toxoplasma gondii</option>
-            <option value="caenorhabditis ">Caenorhabditis elegans</option>
-            <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
-            <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
-            <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
-            <option value="aspergillus_terreus">Aspergillus terreus</option>
-            <option value="botrytis_cinerea ">Botrytis cinerea</option>
-            <option value="candida_albicans ">Candida albicans</option>
-            <option value="candida_guilliermondii ">Candida guilliermondii</option>
-            <option value="candida_tropicalis ">Candida tropicalis</option>
-            <option value="chaetomium_globosum">Chaetomium globosum</option>
-            <option value="coccidioides_immitis ">Coccidioides immitis</option>
-            <option value="coprinus ">Coprinus cinereus</option>
-            <option value="coprinus_cinereus">Coprinus cinereus</option>
-            <option value="cryptococcus_neoformans_gattii ">Cryptococcus neoformans gattii</option>
-            <option value="cryptococcus_neoformans_neoformans_B ">Cryptococcus neoformans neoformans</option>
-            <option value="cryptococcus_neoformans_neoformans_JEC21 ">Cryptococcus neoformans neoformans</option>
-            <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
-            <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
-            <option value="eremothecium_gossypii">Eremothecium gossypii</option>
-            <option value="fusarium_graminearum ">Fusarium graminearum</option>
-            <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
-            <option value="(histoplasma)">Histoplasma capsulatum</option>
-            <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
-            <option value="laccaria_bicolor ">Laccaria bicolor</option>
-            <option value="lamprey">Petromyzon marinus</option>
-            <option value="leishmania_tarentolae">Leishmania tarentolae</option>
-            <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
-            <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
-            <option value="neurospora_crassa">Neurospora crassa</option>
-            <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
-            <option value="pichia_stipitis">Pichia stipitis</option>
-            <option value="rhizopus_oryzae">Rhizopus oryzae</option>
-            <option value="saccharomyces_cerevisiae_S288C ">Saccharomyces cerevisiae</option>
-            <option value="saccharomyces_cerevisiae_rm11-1a_1 ">Saccharomyces cerevisiae</option>
-            <option value="(saccharomyces)">Saccharomyces cerevisiae</option>
-            <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
-            <option value="trichinella">Trichinella spiralis</option>
-            <option value="ustilago_maydis">Ustilago maydis</option>
-            <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
-            <option value="nasonia">Nasonia vitripennis</option>
-            <option value="tomato ">Solanum lycopersicum</option>
-            <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
-            <option value="amphimedon ">Amphimedon queenslandica</option>
-            <option value="pneumocystis ">Pneumocystis jirovecii</option>
-        </param> 
-
-        <param name="strand" type="select" multiple="false" format="text" help="Report predicted genes on both strands, just the forward or just the backward strand.">
-            <option value="both">both</option>
-            <option value="forward">forward</option>
-            <option value="backward">backward</option>
-        </param> 
-
-        <param name="genemodel" label="Gene Model" type="select" multiple="false" format="text" help="Gene Model to predict, for more information please refere to the help.">
-            <option value="complete">complete</option>
-            <option value="partial">partial</option>
-            <option value="intronless">intronless</option>
-            <option value="atleastone">atleastone</option>
-            <option value="exactlyone">exactlyone</option>
-        </param>
-
-	</inputs>
-	<outputs>
-        <data format="gtf" name="output">
-            <change_format>
-                <when input="gff" value="--gff3=on" format="gff" />
-            </change_format>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">augustus</requirement>
-    </requirements>
-    <help>
-
-**What it does**
-
-AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
-It can be used as an ab initio program, which means it bases its prediction purely on the
-sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
-such as EST, MS/MS, protein alignments and synthenic genomic alignments.
-
------	
-
-**Parameters**
-
-Gene Model::
-
-    partial      : allow prediction of incomplete genes at the sequence boundaries (default)
-    intronless   : only predict single-exon genes like in prokaryotes and some eukaryotes
-    complete     : only predict complete genes
-    atleastone   : predict at least one complete gene
-    exactlyone   : predict exactly one complete gene
-
-
-
-**Example**
-
-Suppose you have the following DNA formatted sequences::
-
-    >Seq1
-    cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
-    ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
-    cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
-    cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
-    ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
-
-Running this tool will produce this::
-
-    # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----
-    #
-    # Constraints/Hints:
-    # (none)
-    # Predicted genes for sequence number 1 on both strands
-    # start gene g1
-    scaffold1|size1992969	AUGUSTUS	gene	17453	19382	0.11	+	.	g6
-    scaffold1|size1992969	AUGUSTUS	transcript	17453	19382	0.11	+	.	g6.t1
-    scaffold1|size1992969	AUGUSTUS	start_codon	17453	17455	.	+	0	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	intron	17615	17660	0.38	+	.	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	intron	17708	17772	0.54	+	.	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	intron	17902	18035	0.58	+	.	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	intron	18313	18367	0.99	+	.	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	intron	19014	19080	0.44	+	.	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	CDS	17453	17614	0.55	+	0	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	CDS	17661	17707	0.38	+	0	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	CDS	17773	17901	0.54	+	1	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	CDS	18036	18312	0.52	+	1	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	CDS	18368	19013	0.99	+	0	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	CDS	19081	19379	0.31	+	2	transcript_id "g6.t1"; gene_id "g6";
-    scaffold1|size1992969	AUGUSTUS	stop_codon	19380	19382	.	+	0	transcript_id "g6.t1"; gene_id "g6";
-
-
-**References**
-
-Mario Stanke and Stephan Waack (2003) 
-Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. 
-Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
-
-
-	</help>
-</tool>
diff -r 5663d1a1b29c -r d5d5999ff4f1 augustus/readme.txt
--- a/augustus/readme.txt	Wed Mar 14 17:07:11 2012 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-Galaxy wrapper for Augustus
-=====================================
-
-This wrapper is copyright 2012 by Björn Grüning.
-
-This is a wrapper for the command line tool of augustus.
-http://bioinf.uni-greifswald.de/augustus/
-
-AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
-
-Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
-A novel hybrid gene prediction method employing protein multiple sequence alignments
-Bioinformatics, doi: 10.1093/bioinformatics/btr010
-
-Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
-Using native and syntenically mapped cDNA alignments to improve de novo gene finding
-Bioinformatics, doi: 10.1093/bioinformatics/btn013
-
-Mario Stanke and Stephan Waack (2003)
-Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. 
-Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
-
-
-
-
-Installation
-============
-
-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.
-For example:
-
-<section name="Gene Prediction" id="gene_prediction">
-    <tool file="gene_prediction/tools/augustus/augustus.xml" />
-</section>
-
-
-Set the AUGUSTUS_CONFIG_PATH to /path_to_augustus/augustus/config with
-    export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
-or modify the wrapper and use the following additional commandline switch:
-    --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
-
-
-
-
-History
-=======
-
-v0.1 - Initial public release
-
-
-Wrapper Licence (MIT/BSD style)
-===============================
-
-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 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.
-
diff -r 5663d1a1b29c -r d5d5999ff4f1 augustus/tool_conf.xml
--- a/augustus/tool_conf.xml	Wed Mar 14 17:07:11 2012 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<toolbox>
-  <section name="Gene Prediction" id="gene_prediction">
-        <tool file="gene_prediction/tools/augustus/augustus.xml" />
-  </section>
-</toolbox>
diff -r 5663d1a1b29c -r d5d5999ff4f1 readme.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.txt	Thu Mar 15 10:09:28 2012 +0100
@@ -0,0 +1,78 @@
+Galaxy wrapper for Augustus
+=====================================
+
+This wrapper is copyright 2012 by Björn Grüning.
+
+This is a wrapper for the command line tool of augustus.
+http://bioinf.uni-greifswald.de/augustus/
+
+AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
+
+Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
+A novel hybrid gene prediction method employing protein multiple sequence alignments
+Bioinformatics, doi: 10.1093/bioinformatics/btr010
+
+Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
+Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+Bioinformatics, doi: 10.1093/bioinformatics/btn013
+
+Mario Stanke and Stephan Waack (2003)
+Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. 
+Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
+
+
+
+
+Installation
+============
+
+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.
+For example:
+
+<section name="Gene Prediction" id="gene_prediction">
+    <tool file="gene_prediction/tools/augustus/augustus.xml" />
+</section>
+
+
+Set the AUGUSTUS_CONFIG_PATH to /path_to_augustus/augustus/config with
+    export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+or modify the wrapper and use the following additional commandline switch:
+    --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+
+
+
+
+History
+=======
+
+v0.1 - Initial public release
+
+
+Wrapper Licence (MIT/BSD style)
+===============================
+
+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 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.
+
diff -r 5663d1a1b29c -r d5d5999ff4f1 tool_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_conf.xml	Thu Mar 15 10:09:28 2012 +0100
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<toolbox>
+  <section name="Gene Prediction" id="gene_prediction">
+        <tool file="gene_prediction/tools/augustus/augustus.xml" />
+  </section>
+</toolbox>