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comparison prokka.xml @ 1:2bb7c28ea68f draft

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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
parents 5c0b71c6a2b0
children 5c289bf13a08
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0:5c0b71c6a2b0 1:2bb7c28ea68f
1 <tool id="prokka" name="prokka" version="0.1"> 1 <tool id="prokka" name="prokka" version="0.2">
2 <description>prokaryotic genome annotation</description> 2 <description>prokaryotic genome annotation</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6">prokka</requirement> 4 <requirement type="package" version="1.7">prokka</requirement>
5 <requirement type="package" version="1.2.36">aragorn</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> 6 <requirement type="package" version="2.60">prodigal</requirement>
8 <requirement type="package" version="4.1">signalp</requirement> 7 <requirement type="package" version="0.1">barrnap</requirement>
9 <requirement type="package" version="3.0">infernal</requirement> 8 <!-- <requirement type="package" version="4.1">signalp</requirement> -->
10 <requirement type="package" version="3.1">hmmer</requirement> 9 <!-- <requirement type="package" version="3.0">infernal</requirement> -->
11 <requirement type="package">blast+</requirement> 10 <requirement type="package" version="3.1b1">hmmer</requirement>
11 <requirement type="package" version="2.2.26+">blast+</requirement>
12 <requirement type="package">tbl2asn</requirement> 12 <requirement type="package">tbl2asn</requirement>
13 </requirements> 13 </requirements>
14 <version_command>prokka --version</version_command> 14 <version_command>prokka --version</version_command>
15 <command>prokka --outdir outdir --force 15 <command>prokka --outdir outdir --force
16 --quiet ## To avoid messages written to stderr and causing galaxy errors 16 --quiet ## To avoid messages written to stderr and causing galaxy errors
17 --prefix prokka 17 --prefix prokka
18 $addgenes 18 $addgenes
19 --locustag $locustag 19 --locustag $locustag
20 $compliant
20 --increment $increment 21 --increment $increment
22 #if str($centre) != ""
21 --centre $centre 23 --centre $centre
22 --genus $genus --species $species --strain $strain 24 #end if
25 #if str($genus) != ""
26 --genus $genus
27 #end if
28 #if str($species) != ""
29 --species $species
30 #end if
31 #if str($strain) != ""
32 --strain $strain
33 #end if
34 #if str($plasmid) != ""
35 --plasmid $plasmid
36 #end if
23 --kingdom $kingdom 37 --kingdom $kingdom
24 --gcode $gcode 38 --gcode $gcode
25 #if $gram != "none" 39 #if $gram != "None"
26 --gram $gram 40 --gram $gram
27 #end if 41 #end if
28 $usegenus 42 $usegenus
29 $metagenome 43 $metagenome
30 $fast 44 $fast
31 --cpus $cpus 45 --cpus $cpus
32 --mincontig $mincontig 46 --mincontig $mincontig
33 --evalue $evalue 47 --evalue $evalue
48 $rfam
49 $norrna
50 $notrna
34 $input 51 $input
35 </command> 52 </command>
36 <inputs> 53 <inputs>
37 <param name="input" type="data" format="fasta" label="Contigs to annotate" /> 54 <param name="input" type="data" format="fasta" label="Contigs to annotate" />
38 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix"/> 55 <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" /> 56 <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" /> 57 <param name="increment" type="integer" value="10" label="Locus tag counter increment" />
41 <param name="centre" type="text" value="molevoUU" label="Locus tag prefix"/> 58 <param name="compliant" type="boolean" truevalue="--compliant" falsevalue="" checked="false" label="Force Genbank/ENA/DDJB compliance: --genes --mincontiglen 200 --centre XXX" />
59 <param name="centre" type="text" value="XXX" label="Locus tag prefix"/>
42 <param name="genus" type="text" value="Genus" label="Genus name (will be used to aid annotation)"/> 60 <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"/> 61 <param name="species" type="text" value="species" label="Species name"/>
44 <param name="strain" type="text" value="strain" label="Strain name"/> 62 <param name="strain" type="text" value="strain" label="Strain name"/>
63 <param name="plasmid" type="text" value="" label="Plasmid name or identifier"/>
45 <param name="kingdom" type="select" display="radio" label="Annotation mode"> 64 <param name="kingdom" type="select" display="radio" label="Annotation mode">
46 <option value="Archaea">Archaea</option> 65 <option value="Archaea">Archaea</option>
47 <option value="Bacteria" selected="True">Bacteria</option> 66 <option value="Bacteria" selected="True">Bacteria</option>
48 <option value="Viruses">Viruses</option> 67 <option value="Viruses">Viruses</option>
49 </param> 68 </param>
58 <param name="fast" type="boolean" truevalue="--fast" falsevalue="" checked="false" label="Fast mode - skip CDS /product searching" /> 77 <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] " /> 78 <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]" /> 79 <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" /> 80 <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!)" /> 81 <param name="rfam" type="boolean" truevalue="--rfam" falsevalue="" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
82 <param name="norrna" type="boolean" truevalue="--norrna" falsevalue="" checked="false" label="Don't run rRNA search" />
83 <param name="notrna" type="boolean" truevalue="--notrna" falsevalue="" checked="false" label="Don't run tRNA search" />
63 </inputs> 84 </inputs>
64 <outputs> 85 <outputs>
65 <data name="out_gff" format="gff" label="GFF" from_work_dir="outdir/prokka.gff"/> 86 <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"/> 87 <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"/> 88 <data name="out_faa" format="fasta" label="Proteins (fasta)" from_work_dir="outdir/prokka.faa"/>
72 <data name="out_tbl" format="txt" label="Genbank submission (tbl)" from_work_dir="outdir/prokka.tbl"/> 93 <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"/> 94 <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"/> 95 <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/>
75 </outputs> 96 </outputs>
76 <stdio> 97 <stdio>
77 <exit_code range="1:" level="fatal" description="Error" /> 98 <!--<exit_code range="1:" level="fatal" description="Error" />-->
78 </stdio> 99 <regex match="not a readable non-empty FASTA file"
100 source="stdout"
101 level="fatal"
102 description="Input file not a readable non-empty FASTA file" />
103 </stdio>
104
79 <help> 105 <help>
80 **What it does** 106 **What it does**
81 107
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 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
83 109