annotate prokka.xml @ 7:39bc9c61c55b draft

Uploaded
author lionelguy
date Thu, 05 Sep 2013 07:42:05 -0400
parents 5c289bf13a08
children 37e2aeda27f4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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>
7
39bc9c61c55b Uploaded
lionelguy
parents: 3
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="0.1">barrnap</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="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
10 <!-- <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
11 <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
12 <requirement type="package" version="2.2.26+">blast+</requirement>
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
13 <requirement type="package">tbl2asn</requirement>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
14 </requirements>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
15 <version_command>prokka --version</version_command>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
16 <command>prokka --outdir outdir --force
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
17 --quiet ## To avoid messages written to stderr and causing galaxy errors
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
18 --prefix prokka
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
19 $addgenes
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
20 --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
21 $compliant
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
22 --increment $increment
1
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
23 #if str($centre) != ""
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
24 --centre $centre
1
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
25 #end if
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
26 #if str($genus) != ""
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
27 --genus $genus
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
28 #end if
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
29 #if str($species) != ""
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
30 --species $species
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
31 #end if
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
32 #if str($strain) != ""
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
33 --strain $strain
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
34 #end if
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
35 #if str($plasmid) != ""
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
36 --plasmid $plasmid
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
37 #end if
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
38 --kingdom $kingdom
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
39 --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
40 #if $gram != "None"
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
41 --gram $gram
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
42 #end if
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
43 $usegenus
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
44 $metagenome
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
45 $fast
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
46 --cpus $cpus
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
47 --mincontig $mincontig
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
48 --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
49 $rfam
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
50 $norrna
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
51 $notrna
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
52 $input
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
53 </command>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
54 <inputs>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
55 <param name="input" type="data" format="fasta" label="Contigs to annotate" />
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
56 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
57 <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
58 <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
59 <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
60 <param name="centre" type="text" value="XXX" label="Locus tag prefix"/>
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
61 <param name="genus" type="text" value="Genus" label="Genus name (will be used to aid annotation)"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
62 <param name="species" type="text" value="species" label="Species name"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
63 <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
64 <param name="plasmid" type="text" value="" label="Plasmid name or identifier"/>
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
65 <param name="kingdom" type="select" display="radio" label="Annotation mode">
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
66 <option value="Archaea">Archaea</option>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
67 <option value="Bacteria" selected="True">Bacteria</option>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
68 <option value="Viruses">Viruses</option>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
69 </param>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
70 <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
71 <param name="gram" type="select" display="radio" label="Gram">
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
72 <option selected="true" value="none">N/A</option>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
73 <option value="pos">positive</option>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
74 <option value="neg">negative</option>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
75 </param>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
76 <param name="usegenus" type="boolean" truevalue="--usegenus" falsevalue="" checked="false" label="Use genus-specific BLAST databases" />
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
77 <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
78 <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
79 <param name="cpus" type="integer" value="4" min="1" label="Number of CPUs to use " />
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
80 <param name="mincontig" type="integer" value="200" label="Minimum contig size [NCBI needs 200]" />
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
81 <param name="evalue" type="text" value="1e-06" label="Similarity e-value cut-off" />
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
82 <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
83 <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
84 <param name="notrna" type="boolean" truevalue="--notrna" falsevalue="" checked="false" label="Don't run tRNA search" />
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
85 </inputs>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
86 <outputs>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
87 <data name="out_gff" format="gff" label="GFF" from_work_dir="outdir/prokka.gff"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
88 <data name="out_genbank" format="genbank" label="Genbank" from_work_dir="outdir/prokka.gbk"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
89 <data name="out_faa" format="fasta" label="Proteins (fasta)" from_work_dir="outdir/prokka.faa"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
90 <data name="out_ffn" format="fasta" label="Protein coding genes (fasta)" from_work_dir="outdir/prokka.ffn"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
91 <data name="out_fna" format="fasta" label="Genome (fasta)" from_work_dir="outdir/prokka.fna"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
92 <data name="out_fsa" format="fasta" label="Genbank submission (fasta)" from_work_dir="outdir/prokka.fsa"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
93 <data name="out_sqn" format="txt" label="Genbank submission (sqn)" from_work_dir="outdir/prokka.sqn"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
94 <data name="out_tbl" format="txt" label="Genbank submission (tbl)" from_work_dir="outdir/prokka.tbl"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
95 <data name="out_log" format="txt" label="Log" from_work_dir="outdir/prokka.log"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
96 <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
97 </outputs>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
98 <stdio>
3
5c289bf13a08 Uploaded
lionelguy
parents: 1
diff changeset
99 <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
100 <regex match="not a readable non-empty FASTA file"
3
5c289bf13a08 Uploaded
lionelguy
parents: 1
diff changeset
101 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
102 level="fatal"
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
103 description="Input file not a readable non-empty FASTA file" />
3
5c289bf13a08 Uploaded
lionelguy
parents: 1
diff changeset
104 <regex match="Illegal division by zero"
5c289bf13a08 Uploaded
lionelguy
parents: 1
diff changeset
105 source="both"
5c289bf13a08 Uploaded
lionelguy
parents: 1
diff changeset
106 level="fatal"
5c289bf13a08 Uploaded
lionelguy
parents: 1
diff changeset
107 description="Illegal division by zero" />
7
39bc9c61c55b Uploaded
lionelguy
parents: 3
diff changeset
108 <regex match="no suitable sequence entries"
39bc9c61c55b Uploaded
lionelguy
parents: 3
diff changeset
109 source="both"
39bc9c61c55b Uploaded
lionelguy
parents: 3
diff changeset
110 level="fatal"
39bc9c61c55b Uploaded
lionelguy
parents: 3
diff changeset
111 description="Input contains no suitable sequences" />
39bc9c61c55b Uploaded
lionelguy
parents: 3
diff changeset
112 <regex match="Can't find required"
39bc9c61c55b Uploaded
lionelguy
parents: 3
diff changeset
113 source="both"
39bc9c61c55b Uploaded
lionelguy
parents: 3
diff changeset
114 level="fatal"
39bc9c61c55b Uploaded
lionelguy
parents: 3
diff changeset
115 description="Dependencies not available" />
39bc9c61c55b Uploaded
lionelguy
parents: 3
diff changeset
116
1
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
117 </stdio>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents: 0
diff changeset
118
0
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
119 <help>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
120 **What it does**
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
121
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
122 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
123
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
124 **License**
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
125
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
126 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
127
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
128 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
129
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
130 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
131
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
132 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
133 </help>
5c0b71c6a2b0 Initial version
lionelguy
parents:
diff changeset
134 </tool>