prokka: prokka.xml annotate

annotate prokka.xml @ 9:37e2aeda27f4 draft

Uploaded

author	lionelguy
date	Fri, 06 Sep 2013 02:50:44 -0400
parents	39bc9c61c55b
children	2720b1e27a9c

rev	line source
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	1 <tool id="prokka" name="prokka" version="0.2">
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	2 <description>prokaryotic genome annotation</description>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	3 <requirements>
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	4 <requirement type="package" version="1.7">prokka</requirement>
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	5 <requirement type="package" version="1.2.36">aragorn</requirement>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	6 <requirement type="package" version="2.60">prodigal</requirement>
9 37e2aeda27f4 Uploaded lionelguy parents: 7 diff changeset	7 <requirement type="package" version="0.1">package_barrnap_0_1</requirement>
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	8 <!-- <requirement type="package" version="4.1">signalp</requirement> -->
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	9 <!-- <requirement type="package" version="3.0">infernal</requirement> -->
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	10 <requirement type="package" version="3.1b1">hmmer</requirement>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	11 <requirement type="package" version="2.2.26+">blast+</requirement>
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	12 <requirement type="package">tbl2asn</requirement>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	13 </requirements>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	14 <version_command>prokka --version</version_command>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	15 <command>prokka --outdir outdir --force
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	16 --quiet ## To avoid messages written to stderr and causing galaxy errors
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	17 --prefix prokka
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	18 $addgenes
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	19 --locustag $locustag
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	20 $compliant
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	21 --increment $increment
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	22 #if str($centre) != ""
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	23 --centre $centre
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	24 #end if
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	25 #if str($genus) != ""
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	26 --genus $genus
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	27 #end if
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	28 #if str($species) != ""
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	29 --species $species
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	30 #end if
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	31 #if str($strain) != ""
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	32 --strain $strain
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	33 #end if
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	34 #if str($plasmid) != ""
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	35 --plasmid $plasmid
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	36 #end if
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	37 --kingdom $kingdom
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	38 --gcode $gcode
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	39 #if $gram != "None"
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	40 --gram $gram
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	41 #end if
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	42 $usegenus
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	43 $metagenome
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	44 $fast
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	45 --cpus $cpus
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	46 --mincontig $mincontig
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	47 --evalue $evalue
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	48 $rfam
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	49 $norrna
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	50 $notrna
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	51 $input
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	52 </command>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	53 <inputs>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	54 <param name="input" type="data" format="fasta" label="Contigs to annotate" />
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	55 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	56 <param name="addgenes" type="boolean" truevalue="--addgenes" falsevalue="" checked="false" label="Add 'gene' features for each 'CDS' feature" />
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	57 <param name="increment" type="integer" value="10" label="Locus tag counter increment" />
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	58 <param name="compliant" type="boolean" truevalue="--compliant" falsevalue="" checked="false" label="Force Genbank/ENA/DDJB compliance: --genes --mincontiglen 200 --centre XXX" />
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	59 <param name="centre" type="text" value="XXX" label="Locus tag prefix"/>
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	60 <param name="genus" type="text" value="Genus" label="Genus name (will be used to aid annotation)"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	61 <param name="species" type="text" value="species" label="Species name"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	62 <param name="strain" type="text" value="strain" label="Strain name"/>
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	63 <param name="plasmid" type="text" value="" label="Plasmid name or identifier"/>
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	64 <param name="kingdom" type="select" display="radio" label="Annotation mode">
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	65 <option value="Archaea">Archaea</option>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	66 <option value="Bacteria" selected="True">Bacteria</option>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	67 <option value="Viruses">Viruses</option>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	68 </param>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	69 <param name="gcode" type="integer" value="0" min="0" max="23" label="Genetic code" help="Overrides the annotation mode option if set to > 0"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	70 <param name="gram" type="select" display="radio" label="Gram">
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	71 <option selected="true" value="none">N/A</option>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	72 <option value="pos">positive</option>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	73 <option value="neg">negative</option>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	74 </param>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	75 <param name="usegenus" type="boolean" truevalue="--usegenus" falsevalue="" checked="false" label="Use genus-specific BLAST databases" />
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	76 <param name="metagenome" type="boolean" truevalue="--metagenome" falsevalue="" checked="false" label="Improve gene predictions for highly fragmented genomes" />
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	77 <param name="fast" type="boolean" truevalue="--fast" falsevalue="" checked="false" label="Fast mode - skip CDS /product searching" />
3 5c289bf13a08 Uploaded lionelguy parents: 1 diff changeset	78 <param name="cpus" type="integer" value="4" min="1" label="Number of CPUs to use " />
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	79 <param name="mincontig" type="integer" value="200" label="Minimum contig size [NCBI needs 200]" />
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	80 <param name="evalue" type="text" value="1e-06" label="Similarity e-value cut-off" />
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	81 <param name="rfam" type="boolean" truevalue="--rfam" falsevalue="" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	82 <param name="norrna" type="boolean" truevalue="--norrna" falsevalue="" checked="false" label="Don't run rRNA search" />
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	83 <param name="notrna" type="boolean" truevalue="--notrna" falsevalue="" checked="false" label="Don't run tRNA search" />
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	84 </inputs>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	85 <outputs>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	86 <data name="out_gff" format="gff" label="GFF" from_work_dir="outdir/prokka.gff"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	87 <data name="out_genbank" format="genbank" label="Genbank" from_work_dir="outdir/prokka.gbk"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	88 <data name="out_faa" format="fasta" label="Proteins (fasta)" from_work_dir="outdir/prokka.faa"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	89 <data name="out_ffn" format="fasta" label="Protein coding genes (fasta)" from_work_dir="outdir/prokka.ffn"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	90 <data name="out_fna" format="fasta" label="Genome (fasta)" from_work_dir="outdir/prokka.fna"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	91 <data name="out_fsa" format="fasta" label="Genbank submission (fasta)" from_work_dir="outdir/prokka.fsa"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	92 <data name="out_sqn" format="txt" label="Genbank submission (sqn)" from_work_dir="outdir/prokka.sqn"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	93 <data name="out_tbl" format="txt" label="Genbank submission (tbl)" from_work_dir="outdir/prokka.tbl"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	94 <data name="out_log" format="txt" label="Log" from_work_dir="outdir/prokka.log"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	95 <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	96 </outputs>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	97 <stdio>
3 5c289bf13a08 Uploaded lionelguy parents: 1 diff changeset	98 <exit_code range="1:" level="fatal" description="Error" />
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	99 <regex match="not a readable non-empty FASTA file"
3 5c289bf13a08 Uploaded lionelguy parents: 1 diff changeset	100 source="both"
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	101 level="fatal"
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	102 description="Input file not a readable non-empty FASTA file" />
3 5c289bf13a08 Uploaded lionelguy parents: 1 diff changeset	103 <regex match="Illegal division by zero"
5c289bf13a08 Uploaded lionelguy parents: 1 diff changeset	104 source="both"
5c289bf13a08 Uploaded lionelguy parents: 1 diff changeset	105 level="fatal"
5c289bf13a08 Uploaded lionelguy parents: 1 diff changeset	106 description="Illegal division by zero" />
7 39bc9c61c55b Uploaded lionelguy parents: 3 diff changeset	107 <regex match="no suitable sequence entries"
39bc9c61c55b Uploaded lionelguy parents: 3 diff changeset	108 source="both"
39bc9c61c55b Uploaded lionelguy parents: 3 diff changeset	109 level="fatal"
39bc9c61c55b Uploaded lionelguy parents: 3 diff changeset	110 description="Input contains no suitable sequences" />
39bc9c61c55b Uploaded lionelguy parents: 3 diff changeset	111 <regex match="Can't find required"
39bc9c61c55b Uploaded lionelguy parents: 3 diff changeset	112 source="both"
39bc9c61c55b Uploaded lionelguy parents: 3 diff changeset	113 level="fatal"
39bc9c61c55b Uploaded lionelguy parents: 3 diff changeset	114 description="Dependencies not available" />
39bc9c61c55b Uploaded lionelguy parents: 3 diff changeset	115
1 2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	116 </stdio>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7 lionelguy parents: 0 diff changeset	117
0 5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	118 <help>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	119 What it does
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	120
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	121 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
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	122
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	123 License
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	124
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	125 prokka is developed by Torsten Seemann at Victorian Bioinformatics Consortium http://www.bioinformatics.net.au/. prokka is released under GPLv3 or later.
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	126
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	127 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.
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	128
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	129 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.
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	130
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	131 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	132 </help>
5c0b71c6a2b0 Initial version lionelguy parents: diff changeset	133 </tool>

Mercurial > repos > lionelguy > prokka

annotate prokka.xml @ 9:37e2aeda27f4 draft