Mercurial > repos > abretaudeau > busco
view busco.xml @ 8:c29507d295ae draft
planemo upload
author | abretaudeau |
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date | Wed, 13 Jan 2016 11:27:30 -0500 |
parents | 98ebfba47f7c |
children | 2374b99362ca |
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<tool id="busco" name="Busco" version="1.1b1"> <description>assess genome assembly and annotation completeness</description> <requirements> <requirement type="package" version="1.1b">busco</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command interpreter="python"><![CDATA[ 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 -species ${adv.species} ]]></command> <inputs> <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" /> <param name="lineage" type="select" label="Lineage"> <option value="arthropoda">Arthropoda</option> <option value="bacteria">Bacteria</option> <option value="eukaryota">Eukaryota</option> <option value="fungi">Fungi</option> <option value="metazoa">Metazoa</option> <option value="vertebrata">Vertebrata</option> </param> <param name="mode" type="select" label="Mode"> <option value="all">Genome</option> <option value="Trans">Transcriptome</option> <option value="OGS">Proteome</option> </param> <section name="adv" title="Advanced Options" expanded="False"> <param name="ev" type="float" value="0.01" label="E-value cutoff for BLAST searches."/> <param name="flank" type="integer" value="" optional="True" label="Flanking sequence size for candidate regions" help="If not provided, flank size is calculated based on genome size with a range from 5 to 20 Kbp."/> <param name="species" type="text" value="generic" label="Name of existing Augustus species gene finding metaparameters"/> <param name="long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds ~20h extra run time, but can improve results for some non-model organisms"/> </section> </inputs> <outputs> <data name='busco_sum' format='txt' label="${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"/> <output name="busco_table" file="genome_results/full_table"/> <output name="busco_missing" file="genome_results/missing_buscos_list"/> </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"/> <output name="busco_table" file="proteome_results/full_table"/> <output name="busco_missing" file="proteome_results/missing_buscos_list"/> </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"/> <output name="busco_table" file="transcriptome_results/full_table"/> <output name="busco_missing" file="transcriptome_results/missing_buscos_list"/> </test> </tests> <help> BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs .. _http://busco.ezlab.org/ </help> <citations> <citation type="doi">doi:10.1093/bioinformatics/btv351</citation> </citations> </tool>