| Previous changeset 3:f18f0b887c31 (2018-12-14) Next changeset 5:1440ae06552f (2019-05-13) |
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Commit message:
planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1 |
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modified:
busco.xml |
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| diff -r f18f0b887c31 -r 5ecdeca79a0d busco.xml --- a/busco.xml Fri Dec 14 08:13:25 2018 -0500 +++ b/busco.xml Thu Feb 21 14:33:28 2019 -0500 |
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| @@ -1,45 +1,42 @@ -<tool id="busco" name="Busco" version="3.0.2"> +<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy0"> <description>assess genome assembly and annotation completeness</description> + <macros> + <token name="@TOOL_VERSION@">3.0.2</token> + </macros> <requirements> - <requirement type="package" version="3.0.2">busco</requirement> - <requirement type="package" version="2.2.1">r-ggplot2</requirement> + <requirement type="package" version="@TOOL_VERSION@">busco</requirement> + <requirement type="package" version="3.5.1">r-base</requirement> </requirements> <command><![CDATA[ - export BUSCO_CONFIG_FILE='busco_config.ini' - - && - - if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi && - cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && - export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && +export BUSCO_CONFIG_FILE='busco_config.ini' && +if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi && +cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && +export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && - #if $adv.aug_prediction.augustus_mode == 'history': - ## Using an augustus model from history, we need to unzip it and let augustus find it - - mkdir -p 'augustus_dir/species/' && - - tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null && - #end if +#if $adv.aug_prediction.augustus_mode == 'history': + ## Using an augustus model from history, we need to unzip it and let augustus find it + mkdir -p 'augustus_dir/species/' && + tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null && +#end if - run_BUSCO.py - --in '${input}' - --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}' - --mode '${mode}' - -o "busco_galaxy" - --cpu \${GALAXY_SLOTS:-4} - --evalue ${adv.evalue} - ${adv.long} - --limit ${adv.limit} - #if $adv.aug_prediction.augustus_mode == 'builtin': - --species '${adv.aug_prediction.augustus_species}' - #else if $adv.aug_prediction.augustus_mode == 'history': - --species local - #end if - --tarzip +run_BUSCO.py +--in '${input}' +--lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}' +--mode '${mode}' +-o busco_galaxy +--cpu \${GALAXY_SLOTS:-4} +--evalue ${adv.evalue} +${adv.long} +--limit ${adv.limit} +#if $adv.aug_prediction.augustus_mode == 'builtin': + --species '${adv.aug_prediction.augustus_species}' +#else if $adv.aug_prediction.augustus_mode == 'history': + --species local +#end if +--tarzip ]]></command> <inputs> - <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" /> <param argument="--mode" type="select" label="Mode"> <option value="geno">Genome</option> @@ -224,11 +221,10 @@ </test> </tests> <help> - BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs +BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs - .. _BUSCO: http://busco.ezlab.org/ +.. _BUSCO: http://busco.ezlab.org/ </help> - <citations> <citation type="doi">doi:10.1093/bioinformatics/btv351</citation> </citations> |