Mercurial > repos > lionelguy > prokka
annotate prokka.xml @ 11:f2cc11ac2006 draft default tip
Uploaded
| author | lionelguy |
|---|---|
| date | Fri, 06 Sep 2013 05:39:47 -0400 |
| parents | 2720b1e27a9c |
| children |
| 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 | 2 <description>prokaryotic genome annotation</description> |
| 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 | 5 <requirement type="package" version="1.2.36">aragorn</requirement> |
| 6 <requirement type="package" version="2.60">prodigal</requirement> | |
| 9 | 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> --> |
| 10 | 9 <requirement type="package" version="1.1rc4">infernal</requirement> |
|
1
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 | 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 | |
|
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 | 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 | 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 | 37 --kingdom $kingdom |
| 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 | 40 --gram $gram |
| 41 #end if | |
| 42 $usegenus | |
| 43 $metagenome | |
| 44 $fast | |
| 45 --cpus $cpus | |
| 46 --mincontig $mincontig | |
| 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 | 51 $input |
| 52 </command> | |
| 53 <inputs> | |
| 54 <param name="input" type="data" format="fasta" label="Contigs to annotate" /> | |
| 55 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix"/> | |
| 56 <param name="addgenes" type="boolean" truevalue="--addgenes" falsevalue="" checked="false" label="Add 'gene' features for each 'CDS' feature" /> | |
| 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 | 60 <param name="genus" type="text" value="Genus" label="Genus name (will be used to aid annotation)"/> |
| 61 <param name="species" type="text" value="species" label="Species name"/> | |
| 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 | 64 <param name="kingdom" type="select" display="radio" label="Annotation mode"> |
| 65 <option value="Archaea">Archaea</option> | |
| 66 <option value="Bacteria" selected="True">Bacteria</option> | |
| 67 <option value="Viruses">Viruses</option> | |
| 68 </param> | |
| 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"/> | |
| 70 <param name="gram" type="select" display="radio" label="Gram"> | |
| 71 <option selected="true" value="none">N/A</option> | |
| 72 <option value="pos">positive</option> | |
| 73 <option value="neg">negative</option> | |
| 74 </param> | |
| 75 <param name="usegenus" type="boolean" truevalue="--usegenus" falsevalue="" checked="false" label="Use genus-specific BLAST databases" /> | |
| 76 <param name="metagenome" type="boolean" truevalue="--metagenome" falsevalue="" checked="false" label="Improve gene predictions for highly fragmented genomes" /> | |
| 77 <param name="fast" type="boolean" truevalue="--fast" falsevalue="" checked="false" label="Fast mode - skip CDS /product searching" /> | |
| 3 | 78 <param name="cpus" type="integer" value="4" min="1" label="Number of CPUs to use " /> |
| 0 | 79 <param name="mincontig" type="integer" value="200" label="Minimum contig size [NCBI needs 200]" /> |
| 80 <param name="evalue" type="text" value="1e-06" label="Similarity e-value cut-off" /> | |
| 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 | 84 </inputs> |
| 85 <outputs> | |
| 86 <data name="out_gff" format="gff" label="GFF" from_work_dir="outdir/prokka.gff"/> | |
| 87 <data name="out_genbank" format="genbank" label="Genbank" from_work_dir="outdir/prokka.gbk"/> | |
| 88 <data name="out_faa" format="fasta" label="Proteins (fasta)" from_work_dir="outdir/prokka.faa"/> | |
| 89 <data name="out_ffn" format="fasta" label="Protein coding genes (fasta)" from_work_dir="outdir/prokka.ffn"/> | |
| 90 <data name="out_fna" format="fasta" label="Genome (fasta)" from_work_dir="outdir/prokka.fna"/> | |
| 91 <data name="out_fsa" format="fasta" label="Genbank submission (fasta)" from_work_dir="outdir/prokka.fsa"/> | |
| 92 <data name="out_sqn" format="txt" label="Genbank submission (sqn)" from_work_dir="outdir/prokka.sqn"/> | |
| 93 <data name="out_tbl" format="txt" label="Genbank submission (tbl)" from_work_dir="outdir/prokka.tbl"/> | |
| 94 <data name="out_log" format="txt" label="Log" from_work_dir="outdir/prokka.log"/> | |
| 95 <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/> | |
| 96 </outputs> | |
| 97 <stdio> | |
| 3 | 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 | 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 | 103 <regex match="Illegal division by zero" |
| 104 source="both" | |
| 105 level="fatal" | |
| 106 description="Illegal division by zero" /> | |
| 7 | 107 <regex match="no suitable sequence entries" |
| 108 source="both" | |
| 109 level="fatal" | |
| 110 description="Input contains no suitable sequences" /> | |
| 111 <regex match="Can't find required" | |
| 112 source="both" | |
| 113 level="fatal" | |
| 114 description="Dependencies not available" /> | |
| 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 | 118 <help> |
| 119 **What it does** | |
| 120 | |
| 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 | |
| 122 | |
| 123 **License** | |
| 124 | |
| 125 prokka is developed by Torsten Seemann at Victorian Bioinformatics Consortium http://www.bioinformatics.net.au/. prokka is released under GPLv3 or later. | |
| 126 | |
| 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. | |
| 128 | |
| 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. | |
| 130 | |
| 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/. | |
| 132 </help> | |
| 133 </tool> |