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busco.xml |
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| diff -r 13981b0bc0cb -r a8ddf9d3c14c busco.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/busco.xml Mon Jan 18 10:52:35 2016 -0500 |
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| @@ -0,0 +1,97 @@ +<tool id="busco" name="Busco" version="1.1b1"> + <description>assess genome assembly and annotation completeness</description> + + <requirements> + <requirement type="package" version="1.1b1">busco</requirement> + <requirement type="package" version="3.1">augustus</requirement> + <requirement type="package" version="2.2.31">blast+</requirement> + <requirement type="package" version="3.1b2">hmmer</requirement> + <requirement type="package" version="3.4">python</requirement> + </requirements> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <command><![CDATA[ + python3 \${BUSCO_ROOT_PATH}/BUSCO.py + -in "${input}" + -l "\${BUSCO_DATA_PATH}/${lineage}" + -m "${mode}" + -o "busco_galaxy" + -c \${GALAXY_SLOTS:-4} + -ev ${adv.ev} + ${adv.long} + #if ($adv.flank): + -flank ${adv.flank} + #end if + -sp ${adv.species} + ]]></command> + + <inputs> + + <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" /> + + <param name="lineage" type="select" label="Lineage"> + <option value="arthropoda">Arthropoda</option> + <option value="bacteria">Bacteria</option> + <option value="eukaryota">Eukaryota</option> + <option value="fungi">Fungi</option> + <option value="metazoa">Metazoa</option> + <option value="vertebrata">Vertebrata</option> + </param> + + <param name="mode" type="select" label="Mode"> + <option value="all">Genome</option> + <option value="trans">Transcriptome</option> + <option value="OGS">Proteome</option> + </param> + + <section name="adv" title="Advanced Options" expanded="False"> + <param name="ev" type="float" value="0.01" label="E-value cutoff for BLAST searches."/> + <param name="flank" type="integer" value="" optional="True" label="Flanking sequence size for candidate regions" help="If not provided, flank size is calculated based on genome size with a range from 5 to 20 Kbp."/> + <param name="species" type="text" value="generic" label="Name of existing Augustus species gene finding metaparameters"/> + <param name="long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds ~20h extra run time, but can improve results for some non-model organisms"/> + </section> + </inputs> + <outputs> + <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy"/> + <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy"/> + <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_buscos_list_busco_galaxy"/> + </outputs> + <tests> + <test> + <param name="input" value="genome.fa"/> + <param name="lineage" value="arthropoda"/> + <param name="mode" value="all"/> + <output name="busco_sum" file="genome_results/short_summary" compare="contains"/> + <output name="busco_table" file="genome_results/full_table" compare="contains"/> + <output name="busco_missing" file="genome_results/missing_buscos_list" compare="contains"/> + </test> + <test> + <param name="input" value="proteome.fa"/> + <param name="lineage" value="arthropoda"/> + <param name="mode" value="OGS"/> + <output name="busco_sum" file="proteome_results/short_summary" compare="contains"/> + <output name="busco_table" file="proteome_results/full_table" compare="contains"/> + <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="contains"/> + </test> + <test> + <param name="input" value="transcriptome.fa"/> + <param name="lineage" value="arthropoda"/> + <param name="mode" value="trans"/> + <output name="busco_sum" file="transcriptome_results/short_summary" compare="contains"/> + <output name="busco_table" file="transcriptome_results/full_table" compare="contains"/> + <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="contains"/> + </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> |