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comparison prokka.xml @ 0:5c0b71c6a2b0 draft

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Initial version
author lionelguy
date Tue, 03 Sep 2013 10:15:54 -0400
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children 2bb7c28ea68f
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1 <tool id="prokka" name="prokka" version="0.1">
2 <description>prokaryotic genome annotation</description>
3 <requirements>
4 <requirement type="package" version="1.6">prokka</requirement>
5 <requirement type="package" version="1.2.36">aragorn</requirement>
6 <requirement type="package" version="1.2">rnammer</requirement>
7 <requirement type="package" version="2.60">prodigal</requirement>
8 <requirement type="package" version="4.1">signalp</requirement>
9 <requirement type="package" version="3.0">infernal</requirement>
10 <requirement type="package" version="3.1">hmmer</requirement>
11 <requirement type="package">blast+</requirement>
12 <requirement type="package">tbl2asn</requirement>
13 </requirements>
14 <version_command>prokka --version</version_command>
15 <command>prokka --outdir outdir --force
16 --quiet ## To avoid messages written to stderr and causing galaxy errors
17 --prefix prokka
18 $addgenes
19 --locustag $locustag
20 --increment $increment
21 --centre $centre
22 --genus $genus --species $species --strain $strain
23 --kingdom $kingdom
24 --gcode $gcode
25 #if $gram != "none"
26 --gram $gram
27 #end if
28 $usegenus
29 $metagenome
30 $fast
31 --cpus $cpus
32 --mincontig $mincontig
33 --evalue $evalue
34 $input
35 </command>
36 <inputs>
37 <param name="input" type="data" format="fasta" label="Contigs to annotate" />
38 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix"/>
39 <param name="addgenes" type="boolean" truevalue="--addgenes" falsevalue="" checked="false" label="Add 'gene' features for each 'CDS' feature" />
40 <param name="increment" type="integer" value="10" label="Locus tag counter increment" />
41 <param name="centre" type="text" value="molevoUU" label="Locus tag prefix"/>
42 <param name="genus" type="text" value="Genus" label="Genus name (will be used to aid annotation)"/>
43 <param name="species" type="text" value="species" label="Species name"/>
44 <param name="strain" type="text" value="strain" label="Strain name"/>
45 <param name="kingdom" type="select" display="radio" label="Annotation mode">
46 <option value="Archaea">Archaea</option>
47 <option value="Bacteria" selected="True">Bacteria</option>
48 <option value="Viruses">Viruses</option>
49 </param>
50 <param name="gcode" type="integer" value="0" min="0" max="23" label="Genetic code" help="Overrides the annotation mode option if set to > 0"/>
51 <param name="gram" type="select" display="radio" label="Gram">
52 <option selected="true" value="none">N/A</option>
53 <option value="pos">positive</option>
54 <option value="neg">negative</option>
55 </param>
56 <param name="usegenus" type="boolean" truevalue="--usegenus" falsevalue="" checked="false" label="Use genus-specific BLAST databases" />
57 <param name="metagenome" type="boolean" truevalue="--metagenome" falsevalue="" checked="false" label="Improve gene predictions for highly fragmented genomes" />
58 <param name="fast" type="boolean" truevalue="--fast" falsevalue="" checked="false" label="Fast mode - skip CDS /product searching" />
59 <param name="cpus" type="integer" value="0" min="0" label="Number of CPUs to use [0=all] " />
60 <param name="mincontig" type="integer" value="200" label="Minimum contig size [NCBI needs 200]" />
61 <param name="evalue" type="text" value="1e-06" label="Similarity e-value cut-off" />
62 <param name="rfam" type="boolean" truevalue="--rfam" falsevalue="" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
63 </inputs>
64 <outputs>
65 <data name="out_gff" format="gff" label="GFF" from_work_dir="outdir/prokka.gff"/>
66 <data name="out_genbank" format="genbank" label="Genbank" from_work_dir="outdir/prokka.gbk"/>
67 <data name="out_faa" format="fasta" label="Proteins (fasta)" from_work_dir="outdir/prokka.faa"/>
68 <data name="out_ffn" format="fasta" label="Protein coding genes (fasta)" from_work_dir="outdir/prokka.ffn"/>
69 <data name="out_fna" format="fasta" label="Genome (fasta)" from_work_dir="outdir/prokka.fna"/>
70 <data name="out_fsa" format="fasta" label="Genbank submission (fasta)" from_work_dir="outdir/prokka.fsa"/>
71 <data name="out_sqn" format="txt" label="Genbank submission (sqn)" from_work_dir="outdir/prokka.sqn"/>
72 <data name="out_tbl" format="txt" label="Genbank submission (tbl)" from_work_dir="outdir/prokka.tbl"/>
73 <data name="out_log" format="txt" label="Log" from_work_dir="outdir/prokka.log"/>
74 <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/>
75 </outputs>
76 <stdio>
77 <exit_code range="1:" level="fatal" description="Error" />
78 </stdio>
79 <help>
80 **What it does**
81
82 This wrapper runs prokka, a tool to rapidly annotate prokaryotic genomes. For more information see the tool's homepage: http://www.vicbioinformatics.com/software.prokka.shtml
83
84 **License**
85
86 prokka is developed by Torsten Seemann at Victorian Bioinformatics Consortium http://www.bioinformatics.net.au/. prokka is released under GPLv3 or later.
87
88 This wrapper is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
89
90 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
91
92 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
93 </help>
94 </tool>