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comparison busco.xml @ 0:edb07a3e524e draft

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planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
author iuc
date Thu, 12 Jan 2017 15:12:33 -0500
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1 <tool id="busco" name="Busco" version="2.0">
2 <description>assess genome assembly and annotation completeness</description>
3
4 <requirements>
5 <requirement type="package" version="2.0">busco</requirement>
6 </requirements>
7
8 <command><![CDATA[
9 BUSCO.py
10 --in '${input}'
11 --lineage '${lineage.fields.path}'
12 --mode '${mode}'
13 -o "busco_galaxy"
14 --cpu \${GALAXY_SLOTS:-4}
15 --evalue ${adv.evalue}
16 ${adv.long}
17 --limit ${adv.limit}
18 --species ${adv.species}
19 --tarzip
20 ]]></command>
21
22 <inputs>
23
24 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
25
26 <param argument="--mode" type="select" label="Mode">
27 <option value="geno">Genome</option>
28 <option value="tran">Transcriptome</option>
29 <option value="prot">Proteome</option>
30 </param>
31
32 <param argument="--lineage" type="select" label="Lineage">
33 <options from_data_table="busco">
34 <filter type="sort_by" column="2" />
35 <validator type="no_options" message="No indexes are available" />
36 </options>
37 </param>
38
39 <section name="adv" title="Advanced Options" expanded="False">
40 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
41 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
42 <param argument="--species" type="text" value="generic" label="Name of existing Augustus species gene finding metaparameters"/>
43 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
44 </section>
45 </inputs>
46 <outputs>
47 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/>
48 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy.tsv"/>
49 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/>
50 </outputs>
51 <tests>
52 <test>
53 <param name="input" value="genome.fa"/>
54 <param name="lineage" value="arthropoda_2.0"/>
55 <param name="mode" value="geno"/>
56 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
57 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
58 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
59 </test>
60 <test>
61 <param name="input" value="proteome.fa"/>
62 <param name="lineage" value="arthropoda_2.0"/>
63 <param name="mode" value="prot"/>
64 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/>
65 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/>
66 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
67 </test>
68 <test>
69 <param name="input" value="transcriptome.fa"/>
70 <param name="lineage" value="arthropoda_2.0"/>
71 <param name="mode" value="tran"/>
72 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>
73 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>
74 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
75 </test>
76 </tests>
77 <help>
78 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
79
80 .. _BUSCO: http://busco.ezlab.org/
81 </help>
82
83 <citations>
84 <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
85 </citations>
86 </tool>