Mercurial > repos > crs4 > prokka

annotate prokka.xml @ 9:d004ca37843e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit eb3de6339504064ed4c4fb188d0ef865bbc6cc98
author iuc
date Fri, 28 Oct 2016 13:45:14 -0400
parents 392255fa7ab9
children fd4b2f03cfc6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
1 <tool id="prokka" name="Prokka" version="1.11.1">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
2 <description>prokaryotic genome annotation</description>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
3 <requirements>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
4 <requirement type="package" version="1.11">prokka</requirement>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
5 </requirements>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
6 <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
7 <stdio>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
8 <exit_code range="1:" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
9 </stdio>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
10 <version_command>prokka --version</version_command>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
11 <command><![CDATA[
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
12 prokka
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
13 --cpus \${GALAXY_SLOTS:-8}
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
14 --quiet ## to avoid non-error messages written to stderr
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
15 --outdir outdir --prefix prokka ## used in outputs section
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
16 #if $locustag
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
17 --locustag '$locustag'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
18 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
19 #if str($increment)
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
20 --increment $increment
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
21 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
22 --gffver $gffver
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
23 #if $compliant.compliant_select == "no"
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
24 #if $compliant.addgenes
2
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
parents: 1
diff changeset
25 --addgenes
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
26 #end if
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
27 #if str($compliant.mincontig)
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
28 --mincontig $compliant.mincontig
2
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
parents: 1
diff changeset
29 #end if
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
30 #else
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
31 --compliant
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
32 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
33 #if $centre
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
34 --centre '$centre'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
35 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
36 #if $genus
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
37 --genus '$genus'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
38 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
39 #if $species
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
40 --species '$species'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
41 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
42 #if $strain
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
43 --strain '$strain'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
44 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
45 #if $plasmid
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
46 --plasmid '$plasmid'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
47 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
48 --kingdom $kingdom.kingdom_select
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
49 #if str($kingdom.gcode)
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
50 --gcode $kingdom.gcode
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
51 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
52 #if $usegenus
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
53 --usegenus
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
54 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
55 #if $proteins
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
56 --proteins '$proteins'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
57 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
58 #if $metagenome
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
59 --metagenome
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
60 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
61 #if $fast
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
62 --fast
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
63 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
64 #if str($evalue)
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
65 --evalue $evalue
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
66 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
67 #if $rfam
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
68 --rfam
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
69 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
70 #if $norrna
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
71 --norrna
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
72 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
73 #if $notrna
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
74 --notrna
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
75 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
76 $input
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
77 ]]></command>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
78 <inputs>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
79 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
80 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
81 <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
82 <param name="gffver" type="select" label="GFF version (--gffver)">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
83 <option value="3">3</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
84 <option value="2">2</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
85 <option value="1">1</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
86 </param>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
87 <conditional name="compliant">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
88 <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance (--compliant)" help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below)">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
89 <option value="no">No</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
90 <option value="yes">Yes</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
91 </param>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
92 <when value="no">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
93 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
94 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
95 </when>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
96 <when value="yes" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
97 </conditional>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
98 <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
99 <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
100 <param name="species" type="text" value="" label="Species name (--species)" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
101 <param name="strain" type="text" value="" label="Strain name (--strain)" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
102 <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
103 <conditional name="kingdom">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
104 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
105 <option value="Archaea">Archaea</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
106 <option value="Bacteria" selected="true">Bacteria</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
107 <option value="Viruses">Viruses</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
108 </param>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
109 <when value="Archaea">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
110 <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
111 </when>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
112 <when value="Bacteria">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
113 <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
114 <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
115 <option selected="true" value="none">N/A</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
116 <option value="pos">positive</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
117 <option value="neg">negative</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
118 </param> SignalP is not FOSS -->
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
119 </when>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
120 <when value="Viruses">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
121 <param name="gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
122 </when>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
123 </conditional>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
124 <param name="usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database (--usegenus)" help="Will use the BLAST database for the genus specified above, if installed" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
125 <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
126 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
127 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
128 <param name="evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
129 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
130 <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
131 <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
132
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
133 <param name="outputs" type="select" multiple="true" label="Additional outputs">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
134 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
135 <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
136 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
137 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
138 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
139 <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
140 <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
141 <option value="tbl" selected="True">Feature Table file</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
142 <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
143 <option value="txt" selected="True">Statistics relating to the annotated features found</option>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
144 </param>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
145
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
146 </inputs>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
147 <outputs>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
148 <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
149 <filter>'gff' in outputs</filter>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
150 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
151 <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
152 <filter>'gbk' in outputs</filter>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
153 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
154 <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
155 <filter>'fna' in outputs</filter>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
156 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
157 <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
158 <filter>'faa' in outputs</filter>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
159 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
160 <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
161 <filter>'ffn' in outputs</filter>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
162 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
163 <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
164 <filter>'sqn' in outputs</filter>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
165 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
166 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
167 <filter>'fsa' in outputs</filter>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
168 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
169 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
170 <filter>'tbl' in outputs</filter>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
171 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
172 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
173 <filter>'err' in outputs</filter>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
174 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
175 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
176 <filter>'txt' in outputs</filter>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
177 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
178 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
179 </outputs>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
180 <tests>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
181 <test>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
182 <param name="input" ftype="fasta" value="phiX174.fasta" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
183 <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,err,txt" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
184 <output name="out_gff" file="out.gff" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
185 <output name="out_gbk" file="out.gbk" lines_diff="14" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
186 <output name="out_fna" file="out.fna" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
187 <output name="out_faa" file="out.faa" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
188 <output name="out_ffn" file="out.ffn" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
189 <output name="out_sqn" file="out.sqn" lines_diff="84" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
190 <output name="out_fsa" file="out.fsa" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
191 <output name="out_tbl" file="out.tbl" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
192 <output name="out.err" file="out.err" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
193 <output name="out_txt" file="out.txt" />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
194 <output name="out_log">
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
195 <assert_contents>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
196 <has_text text="Type 'prokka --citation' for more details." />
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
197 </assert_contents>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
198 </output>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
199 </test>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
200 </tests>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
201 <help><![CDATA[
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
202 **What it does**
95505a9fa26f Uploaded
crs4
parents:
diff changeset
203
2
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
parents: 1
diff changeset
204 Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ.
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
205
95505a9fa26f Uploaded
crs4
parents:
diff changeset
206 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
95505a9fa26f Uploaded
crs4
parents:
diff changeset
207
95505a9fa26f Uploaded
crs4
parents:
diff changeset
208 **Output files**
95505a9fa26f Uploaded
crs4
parents:
diff changeset
209
1
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
210 Prokka creates several output files:
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
211
1
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
212 gff
2
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
parents: 1
diff changeset
213 This is the master annotation in GFF format, containing both sequences and annotations
1
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
214 gbk
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
215 This is a standard GenBank file derived from the master .gff . If the input to prokka was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
216 fna
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
217 Nucleotide FASTA file of the input contig sequences
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
218 faa
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
219 Protein FASTA file of the translated CDS sequences
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
220 ffn
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
221 Nucleotide FASTA file of all the annotated sequences, not just CDS
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
222 sqn
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
223 An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
224 fsa
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
225 Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
226 tbl
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
227 Feature Table file, used by "tbl2asn" to create the .sqn file
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
228 err
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
229 Unacceptable annotations - the NCBI discrepancy report
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
230 log
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
231 Contains all the output that Prokka produced during its run
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
232 txt
4b6f16a79fe4 Add txt output file.
crs4
parents: 0
diff changeset
233 Statistics relating to the annotated features found
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
234
95505a9fa26f Uploaded
crs4
parents:
diff changeset
235 **License and citation**
95505a9fa26f Uploaded
crs4
parents:
diff changeset
236
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
237 This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
238
95505a9fa26f Uploaded
crs4
parents:
diff changeset
239 .. _CRS4 Srl.: http://www.crs4.it/
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
240 .. _Earlham Institute: http://earlham.ac.uk/
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
241 .. _MIT license: https://opensource.org/licenses/MIT
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
242
6
3ad7ef0ba385 Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.
crs4
parents: 4
diff changeset
243 You can use this tool only if you agree to the license terms of: `Prokka`_.
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
244
95505a9fa26f Uploaded
crs4
parents:
diff changeset
245 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
246 ]]></help>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
247 <citations>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
248 <citation type="doi">10.1093/bioinformatics/btu135</citation>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
249 <citation type="doi">10.1093/bioinformatics/btu153</citation>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
250 </citations>
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
251 </tool>