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annotate busco.xml @ 1:0b9b7d845c2a draft

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author iuc
date Tue, 24 Jan 2017 12:08:26 -0500
parents edb07a3e524e
children d010a90f588e
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1 <tool id="busco" name="Busco" version="2.0">
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2 <description>assess genome assembly and annotation completeness</description>
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3
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4 <requirements>
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5 <requirement type="package" version="2.0">busco</requirement>
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6 </requirements>
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7
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8 <command><![CDATA[
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9 BUSCO.py
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10 --in '${input}'
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11 --lineage '${lineage.fields.path}'
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12 --mode '${mode}'
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13 -o "busco_galaxy"
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14 --cpu \${GALAXY_SLOTS:-4}
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15 --evalue ${adv.evalue}
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16 ${adv.long}
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17 --limit ${adv.limit}
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18 #if $adv.species:
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19 --species '${adv.species}'
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20 #end if
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21 --tarzip
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22 ]]></command>
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23
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24 <inputs>
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25
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26 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
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27
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28 <param argument="--mode" type="select" label="Mode">
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29 <option value="geno">Genome</option>
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30 <option value="tran">Transcriptome</option>
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31 <option value="prot">Proteome</option>
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32 </param>
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33
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34 <param argument="--lineage" type="select" label="Lineage">
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35 <options from_data_table="busco">
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36 <filter type="sort_by" column="2" />
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37 <validator type="no_options" message="No indexes are available" />
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38 </options>
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39 </param>
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40
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41 <section name="adv" title="Advanced Options" expanded="False">
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42 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
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43 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
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44 <param argument="--species" type="text" optional="True" label="Name of existing Augustus species gene finding metaparameters"/>
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45 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
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46 </section>
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47 </inputs>
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48 <outputs>
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49 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/>
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50 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy.tsv"/>
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51 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="input" value="genome.fa"/>
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56 <param name="lineage" value="arthropoda_2.0"/>
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57 <param name="mode" value="geno"/>
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58 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
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59 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
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60 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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61 </test>
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62 <test>
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63 <param name="input" value="proteome.fa"/>
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64 <param name="lineage" value="arthropoda_2.0"/>
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65 <param name="mode" value="prot"/>
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66 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/>
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67 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/>
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68 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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69 </test>
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70 <test>
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71 <param name="input" value="transcriptome.fa"/>
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72 <param name="lineage" value="arthropoda_2.0"/>
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73 <param name="mode" value="tran"/>
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74 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>
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75 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>
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76 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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77 </test>
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78 </tests>
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79 <help>
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80 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
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81
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82 .. _BUSCO: http://busco.ezlab.org/
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83 </help>
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84
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85 <citations>
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86 <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
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87 </citations>
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88 </tool>