annotate prokka.xml @ 1:2bb7c28ea68f draft

Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
author lionelguy
date Wed, 04 Sep 2013 11:33:13 -0400
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1 <tool id="prokka" name="prokka" version="0.2">
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2 <description>prokaryotic genome annotation</description>
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3 <requirements>
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4 <requirement type="package" version="1.7">prokka</requirement>
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5 <requirement type="package" version="1.2.36">aragorn</requirement>
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6 <requirement type="package" version="2.60">prodigal</requirement>
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7 <requirement type="package" version="0.1">barrnap</requirement>
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8 <!-- <requirement type="package" version="4.1">signalp</requirement> -->
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9 <!-- <requirement type="package" version="3.0">infernal</requirement> -->
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10 <requirement type="package" version="3.1b1">hmmer</requirement>
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11 <requirement type="package" version="2.2.26+">blast+</requirement>
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12 <requirement type="package">tbl2asn</requirement>
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13 </requirements>
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14 <version_command>prokka --version</version_command>
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15 <command>prokka --outdir outdir --force
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16 --quiet ## To avoid messages written to stderr and causing galaxy errors
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17 --prefix prokka
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18 $addgenes
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19 --locustag $locustag
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20 $compliant
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21 --increment $increment
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22 #if str($centre) != ""
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23 --centre $centre
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24 #end if
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25 #if str($genus) != ""
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26 --genus $genus
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27 #end if
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28 #if str($species) != ""
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29 --species $species
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30 #end if
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31 #if str($strain) != ""
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32 --strain $strain
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33 #end if
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34 #if str($plasmid) != ""
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35 --plasmid $plasmid
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36 #end if
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37 --kingdom $kingdom
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38 --gcode $gcode
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39 #if $gram != "None"
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40 --gram $gram
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41 #end if
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42 $usegenus
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43 $metagenome
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44 $fast
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45 --cpus $cpus
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46 --mincontig $mincontig
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47 --evalue $evalue
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48 $rfam
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49 $norrna
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50 $notrna
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51 $input
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52 </command>
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53 <inputs>
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54 <param name="input" type="data" format="fasta" label="Contigs to annotate" />
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55 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix"/>
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56 <param name="addgenes" type="boolean" truevalue="--addgenes" falsevalue="" checked="false" label="Add 'gene' features for each 'CDS' feature" />
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57 <param name="increment" type="integer" value="10" label="Locus tag counter increment" />
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58 <param name="compliant" type="boolean" truevalue="--compliant" falsevalue="" checked="false" label="Force Genbank/ENA/DDJB compliance: --genes --mincontiglen 200 --centre XXX" />
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59 <param name="centre" type="text" value="XXX" label="Locus tag prefix"/>
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60 <param name="genus" type="text" value="Genus" label="Genus name (will be used to aid annotation)"/>
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61 <param name="species" type="text" value="species" label="Species name"/>
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62 <param name="strain" type="text" value="strain" label="Strain name"/>
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63 <param name="plasmid" type="text" value="" label="Plasmid name or identifier"/>
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64 <param name="kingdom" type="select" display="radio" label="Annotation mode">
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65 <option value="Archaea">Archaea</option>
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66 <option value="Bacteria" selected="True">Bacteria</option>
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67 <option value="Viruses">Viruses</option>
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68 </param>
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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"/>
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70 <param name="gram" type="select" display="radio" label="Gram">
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71 <option selected="true" value="none">N/A</option>
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72 <option value="pos">positive</option>
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73 <option value="neg">negative</option>
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74 </param>
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75 <param name="usegenus" type="boolean" truevalue="--usegenus" falsevalue="" checked="false" label="Use genus-specific BLAST databases" />
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76 <param name="metagenome" type="boolean" truevalue="--metagenome" falsevalue="" checked="false" label="Improve gene predictions for highly fragmented genomes" />
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77 <param name="fast" type="boolean" truevalue="--fast" falsevalue="" checked="false" label="Fast mode - skip CDS /product searching" />
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78 <param name="cpus" type="integer" value="0" min="0" label="Number of CPUs to use [0=all] " />
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79 <param name="mincontig" type="integer" value="200" label="Minimum contig size [NCBI needs 200]" />
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80 <param name="evalue" type="text" value="1e-06" label="Similarity e-value cut-off" />
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81 <param name="rfam" type="boolean" truevalue="--rfam" falsevalue="" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
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82 <param name="norrna" type="boolean" truevalue="--norrna" falsevalue="" checked="false" label="Don't run rRNA search" />
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83 <param name="notrna" type="boolean" truevalue="--notrna" falsevalue="" checked="false" label="Don't run tRNA search" />
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84 </inputs>
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85 <outputs>
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86 <data name="out_gff" format="gff" label="GFF" from_work_dir="outdir/prokka.gff"/>
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87 <data name="out_genbank" format="genbank" label="Genbank" from_work_dir="outdir/prokka.gbk"/>
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88 <data name="out_faa" format="fasta" label="Proteins (fasta)" from_work_dir="outdir/prokka.faa"/>
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89 <data name="out_ffn" format="fasta" label="Protein coding genes (fasta)" from_work_dir="outdir/prokka.ffn"/>
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90 <data name="out_fna" format="fasta" label="Genome (fasta)" from_work_dir="outdir/prokka.fna"/>
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91 <data name="out_fsa" format="fasta" label="Genbank submission (fasta)" from_work_dir="outdir/prokka.fsa"/>
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92 <data name="out_sqn" format="txt" label="Genbank submission (sqn)" from_work_dir="outdir/prokka.sqn"/>
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93 <data name="out_tbl" format="txt" label="Genbank submission (tbl)" from_work_dir="outdir/prokka.tbl"/>
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94 <data name="out_log" format="txt" label="Log" from_work_dir="outdir/prokka.log"/>
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95 <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/>
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96 </outputs>
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97 <stdio>
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98 <!--<exit_code range="1:" level="fatal" description="Error" />-->
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99 <regex match="not a readable non-empty FASTA file"
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100 source="stdout"
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101 level="fatal"
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102 description="Input file not a readable non-empty FASTA file" />
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103 </stdio>
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104
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105 <help>
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106 **What it does**
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107
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108 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
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109
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110 **License**
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111
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112 prokka is developed by Torsten Seemann at Victorian Bioinformatics Consortium http://www.bioinformatics.net.au/. prokka is released under GPLv3 or later.
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113
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114 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.
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115
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116 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.
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117
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118 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
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119 </help>
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120 </tool>