| Previous changeset 1:e2b822d7408f (2013-12-05) Next changeset 3:f5075dee9d6b (2015-05-22) |
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augustus.xml tool_conf.xml tool_dependencies.xml |
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| diff -r e2b822d7408f -r a77a4e9921e0 augustus.xml --- a/augustus.xml Thu Dec 05 09:44:17 2013 -0500 +++ b/augustus.xml Wed May 06 14:31:02 2015 -0400 |
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| @@ -3,9 +3,15 @@ <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> </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> <command> +<![CDATA[ ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external script is used to extract the sequences into additional files @@ -14,7 +20,7 @@ --strand=$strand $noInFrameStop $gff - + #if 'protein' in str($outputs).split(','): --protein=on #else: @@ -26,7 +32,7 @@ #else: --codingseq=off #end if - + #if 'introns' in str($outputs).split(','): --introns=on #else: @@ -58,9 +64,9 @@ --genemodel=$genemodel --species=$organism ##--outfile=$output - | tee $output + | tee $output #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','): - | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py + | python $__tool_directory__/extract_features.py #if 'protein' in str($outputs).split(','): --protein $protein_output #end if @@ -68,6 +74,7 @@ --codingseq $codingseq_output #end if #end if +]]> </command> <inputs> <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> @@ -136,13 +143,13 @@ <option value="cacao">Theobroma cacao (cacao)</option> <option value="heliconius_melpomene1">Heliconius melpomene</option> <option value="xenoturbella">Xenoturbella</option> - </param> + </param> <param name="strand" type="select" multiple="false" format="text" help="Report predicted genes on both strands, just the forward or just the backward strand."> <option value="both">both</option> <option value="forward">forward</option> <option value="backward">backward</option> - </param> + </param> <param name="genemodel" label="Gene Model" type="select" multiple="false" format="text" help="Gene Model to predict, for more information please refere to the help."> <option value="complete">complete</option> @@ -213,6 +220,7 @@ </test> </tests> <help> +<![CDATA[ **What it does** @@ -271,12 +279,9 @@ scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6"; -**References** - -Mario Stanke and Stephan Waack (2003) -Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. -Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225 - - +]]> </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btg1080</citation> + </citations> </tool> |
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| diff -r e2b822d7408f -r a77a4e9921e0 tool_dependencies.xml --- a/tool_dependencies.xml Thu Dec 05 09:44:17 2013 -0500 +++ b/tool_dependencies.xml Wed May 06 14:31:02 2015 -0400 |
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| @@ -1,12 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <set_environment version="1.0"> - <environment_variable name="AUGUSTUS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> <package name="augustus" version="2.7"> <install version="1.0"> <actions> - <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.7.tar.gz</action> + <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus.2.7.tar.gz</action> <action type="shell_command">make</action> <action type="move_directory_files"> <source_directory>bin</source_directory> |