comparison busco.xml @ 4:5ecdeca79a0d draft

planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1

3:f18f0b887c31

<tool id="busco" name="Busco" version="3.0.2">
    <description>assess genome assembly and annotation completeness</description>
    <requirements>
        <requirement type="package" version="3.0.2">busco</requirement>
        <requirement type="package" version="2.2.1">r-ggplot2</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/ &&

        #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
    ]]></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>
            <option value="tran">Transcriptome</option>
            <option value="prot">Proteome</option>

            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
        </test>
    </tests>
    <help>
        BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

        .. _BUSCO: http://busco.ezlab.org/
    </help>

     <citations>
        <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
    </citations>
</tool>

4:5ecdeca79a0d

<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="@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/ &&

#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
    ]]></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>
            <option value="tran">Transcriptome</option>
            <option value="prot">Proteome</option>

            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
        </test>
    </tests>
    <help>
BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

.. _BUSCO: http://busco.ezlab.org/
    </help>
     <citations>
        <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
    </citations>
</tool>