Mercurial > repos > iuc > busco

annotate busco.xml @ 1:87983967544b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit c8dc021bd99764eacaa17cbe4f44bcdacca00414
author iuc
date Tue, 24 Jan 2017 12:08:38 -0500
parents 5e3543b1ef9f
children 382a4c19007f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
1 <tool id="busco" name="Busco" version="2.0">
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
2 <description>assess genome assembly and annotation completeness</description>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
3
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
4 <requirements>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
5 <requirement type="package" version="2.0">busco</requirement>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
6 </requirements>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
7
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
8 <command><![CDATA[
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
9 BUSCO.py
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
10 --in '${input}'
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
11 --lineage '${lineage.fields.path}'
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
12 --mode '${mode}'
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
13 -o "busco_galaxy"
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
14 --cpu \${GALAXY_SLOTS:-4}
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
15 --evalue ${adv.evalue}
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
16 ${adv.long}
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
17 --limit ${adv.limit}
1
87983967544b planemo upload commit c8dc021bd99764eacaa17cbe4f44bcdacca00414
iuc
parents: 0
diff changeset
18 #if $adv.species:
87983967544b planemo upload commit c8dc021bd99764eacaa17cbe4f44bcdacca00414
iuc
parents: 0
diff changeset
19 --species '${adv.species}'
87983967544b planemo upload commit c8dc021bd99764eacaa17cbe4f44bcdacca00414
iuc
parents: 0
diff changeset
20 #end if
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
21 --tarzip
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
22 ]]></command>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
23
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
24 <inputs>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
25
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
26 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
27
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
28 <param argument="--mode" type="select" label="Mode">
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
29 <option value="geno">Genome</option>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
30 <option value="tran">Transcriptome</option>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
31 <option value="prot">Proteome</option>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
32 </param>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
33
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
34 <param argument="--lineage" type="select" label="Lineage">
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
35 <options from_data_table="busco">
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
36 <filter type="sort_by" column="2" />
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
37 <validator type="no_options" message="No indexes are available" />
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
38 </options>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
39 </param>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
40
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
41 <section name="adv" title="Advanced Options" expanded="False">
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
42 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
43 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
1
87983967544b planemo upload commit c8dc021bd99764eacaa17cbe4f44bcdacca00414
iuc
parents: 0
diff changeset
44 <param argument="--species" type="text" optional="True" label="Name of existing Augustus species gene finding metaparameters"/>
0
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
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"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
46 </section>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
47 </inputs>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
48 <outputs>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
49 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
50 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy.tsv"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
51 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
52 </outputs>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
53 <tests>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
54 <test>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
55 <param name="input" value="genome.fa"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
56 <param name="lineage" value="arthropoda_2.0"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
57 <param name="mode" value="geno"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
58 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
59 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
60 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
61 </test>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
62 <test>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
63 <param name="input" value="proteome.fa"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
64 <param name="lineage" value="arthropoda_2.0"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
65 <param name="mode" value="prot"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
66 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
67 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
68 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
69 </test>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
70 <test>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
71 <param name="input" value="transcriptome.fa"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
72 <param name="lineage" value="arthropoda_2.0"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
73 <param name="mode" value="tran"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
74 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
75 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
76 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
77 </test>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
78 </tests>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
79 <help>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
80 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
81
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
82 .. _BUSCO: http://busco.ezlab.org/
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
83 </help>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
84
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
85 <citations>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
86 <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
87 </citations>
5e3543b1ef9f planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08
iuc
parents:
diff changeset
88 </tool>