Mercurial > repos > crs4 > prokka

annotate prokka.xml @ 18:d643e3b03500 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 442b1247ee31ec9872633be18784f346e4762486"
author iuc
date Sat, 13 Feb 2021 11:58:58 +0000
parents 111884f0d912
children 8a22554cdde2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
1 <tool id="prokka" name="Prokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
parents: 13
diff changeset
2 <description>Prokaryotic genome annotation</description>
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
3 <macros>
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
4 <token name="@TOOL_VERSION@">1.14.6</token>
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
6 </macros>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
7 <requirements>
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">prokka</requirement>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
9 </requirements>
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
parents: 13
diff changeset
10
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
11 <version_command>prokka --version</version_command>
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
parents: 13
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
13 prokka
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
14 --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
15 --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
16 --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
17 #if $locustag
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
18 --locustag '$locustag'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
19 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
20 #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
21 --increment $increment
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
22 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
23 --gffver $gffver
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.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
25 #if $compliant.addgenes
2
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
parents: 1
diff changeset
26 --addgenes
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
27 #end if
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
28 #if str($compliant.mincontig)
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
29 --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
30 #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
31 #else
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
32 --compliant
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
33 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
34 #if $centre
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
35 --centre '$centre'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
36 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
37 #if $genus
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
38 --genus '$genus'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
39 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
40 #if $species
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
41 --species '$species'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
42 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
43 #if $strain
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
44 --strain '$strain'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
45 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
46 #if $plasmid
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
47 --plasmid '$plasmid'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
48 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
49 --kingdom $kingdom.kingdom_select
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
50 #if str($kingdom.gcode)
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
51 --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
52 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
53 #if $usegenus
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
54 --usegenus
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
55 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
56 #if $proteins
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
57 --proteins '$proteins'
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
58 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
59 #if $metagenome
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
60 --metagenome
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
61 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
62 #if $fast
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
63 --fast
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
64 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
65 #if str($evalue)
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
66 --evalue $evalue
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
67 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
68 #if $rfam
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
69 --rfam
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
70 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
71 #if $norrna
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
72 --norrna
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
73 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
74 #if $notrna
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
75 --notrna
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
76 #end if
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
77 $input
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
78 ]]></command>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
79 <inputs>
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="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
81 <param argument="--locustag" type="text" value="" label="Locus tag prefix" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
82 <param argument="--increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
83 <param argument="--gffver" type="select" label="GFF version">
8
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="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
85 <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
86 <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
87 </param>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
88 <conditional name="compliant">
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
89 <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance"
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
90 help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below) (--compliant)">
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
91 <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
92 <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
93 </param>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
94 <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
95 <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
96 <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
97 </when>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
98 <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
99 </conditional>
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
100 <param argument="--centre" type="text" value="" label="Sequencing centre ID" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
101 <param argument="--genus" type="text" value="" label="Genus name" help="May be used to aid annotation, see --usegenus below" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
102 <param argument="--species" type="text" value="" label="Species name" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
103 <param argument="--strain" type="text" value="" label="Strain name" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
104 <param argument="--plasmid" type="text" value="" label="Plasmid name or identifier" />
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
105 <conditional name="kingdom">
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
106 <param name="kingdom_select" type="select" label="Kingdom" help="(--kingdom)">
8
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="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
108 <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
109 <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
110 </param>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
111 <when value="Archaea">
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
112 <param argument="--gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
113 </when>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
114 <when value="Bacteria">
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
115 <param argument="--gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
116 <!-- <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
117 <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
118 <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
119 <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
120 </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
121 </when>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
122 <when value="Viruses">
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
123 <param argument="--gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
124 </when>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
125 </conditional>
18
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
126 <param argument="--usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database" help="Will use the BLAST database for the genus specified above, if installed" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
127 <param argument="--proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
128 <param argument="--metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes" help="Will set --meta option for Prodigal" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
129 <param argument="--fast" type="boolean" checked="false" label="Fast mode" help="Skip CDS /product searching" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
130 <param argument="--evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
131 <param argument="--rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
132 <param argument="--norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
d643e3b03500 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
iuc
parents: 17
diff changeset
133 <param argument="--notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
134
11
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
135 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
136 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option>
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
137 <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 (.gbk)</option>
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
138 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option>
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
139 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option>
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
140 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option>
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
141 <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. (.sqn)</option>
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
142 <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines (.fsa)</option>
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
143 <option value="tbl" selected="True">Feature Table file (.tbl)</option>
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
parents: 13
diff changeset
144 <option value="tsv" selected="True">Annotations in tabular format including COGs etc.</option>
11
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
145 <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option>
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
146 <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
147 </param>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
148
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
149 </inputs>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
150 <outputs>
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_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
12
da479161bbe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 11
diff changeset
152 <filter>outputs and 'gff' in outputs</filter>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
153 </data>
17
111884f0d912 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit e421c38873daaad1ee5e4e3ad59b38cb6bb34253"
iuc
parents: 16
diff changeset
154 <data name="out_gbk" format="genbank" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
12
da479161bbe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 11
diff changeset
155 <filter>outputs and 'gbk' in outputs</filter>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
156 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
157 <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">
12
da479161bbe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 11
diff changeset
158 <filter>outputs and 'fna' in outputs</filter>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
159 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
160 <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">
12
da479161bbe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 11
diff changeset
161 <filter>outputs and 'faa' in outputs</filter>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
162 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
163 <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">
12
da479161bbe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 11
diff changeset
164 <filter>outputs and 'ffn' in outputs</filter>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
165 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
166 <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">
12
da479161bbe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 11
diff changeset
167 <filter>outputs and 'sqn' in outputs</filter>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
168 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
169 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">
12
da479161bbe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 11
diff changeset
170 <filter>outputs and 'fsa' in outputs</filter>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
171 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
172 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
12
da479161bbe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 11
diff changeset
173 <filter>outputs and 'tbl' in outputs</filter>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
174 </data>
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
parents: 13
diff changeset
175 <data name="out_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv" from_work_dir="outdir/prokka.tsv">
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
parents: 13
diff changeset
176 <filter>outputs and 'tsv' in outputs</filter>
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
parents: 13
diff changeset
177 </data>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
178 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
12
da479161bbe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 11
diff changeset
179 <filter>outputs and 'err' in outputs</filter>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
180 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
181 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">
12
da479161bbe4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 11
diff changeset
182 <filter>outputs and 'txt' in outputs</filter>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
183 </data>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
184 <data name="out_log" format="txt" label="${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
185 </outputs>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
186 <tests>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
187 <test>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
188 <param name="input" ftype="fasta" value="phiX174.fasta" />
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
parents: 13
diff changeset
189 <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" />
8
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_gff" file="out.gff" />
15
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
191 <output name="out_gbk" >
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
192 <assert_contents>
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
193 <has_text_matching expression="LOCUS" />
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
194 <has_text_matching expression="//" />
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
195 </assert_contents>
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
196 </output>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
197 <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
198 <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
199 <output name="out_ffn" file="out.ffn" />
15
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
200 <output name="out_sqn" >
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
201 <assert_contents>
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
202 <has_text_matching expression="Seq-entry" />
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
203 <has_text_matching expression="contig2" />
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
204 </assert_contents>
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
205 </output>
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
206 <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
207 <output name="out_tbl" file="out.tbl" />
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
parents: 13
diff changeset
208 <output name="out_tsv" file="out.tsv" />
15
3a0bd09a41dd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit f64c36610e6ca2240e4d745a5708d0d02ba4a16d"
iuc
parents: 14
diff changeset
209 <output name="out_err" file="out.err" lines_diff="14" />
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
210 <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
211 <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
212 <assert_contents>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
213 <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
214 </assert_contents>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
215 </output>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
216 </test>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
217 </tests>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
218 <help><![CDATA[
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
219 **What it does**
95505a9fa26f Uploaded
crs4
parents:
diff changeset
220
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
221 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
222
13
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
iuc
parents: 12
diff changeset
223 .. _Prokka: http://github.com/tseemann/prokka
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
224
95505a9fa26f Uploaded
crs4
parents:
diff changeset
225 **Output files**
95505a9fa26f Uploaded
crs4
parents:
diff changeset
226
11
fd4b2f03cfc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
iuc
parents: 8
diff changeset
227 Prokka creates several output files, which are described in the **Additional outputs** section above.
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
228
95505a9fa26f Uploaded
crs4
parents:
diff changeset
229 **License and citation**
95505a9fa26f Uploaded
crs4
parents:
diff changeset
230
14
eaee459f3d69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
iuc
parents: 13
diff changeset
231 This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_, 2018 `Galaxy IUC` and is released under the `MIT license`_.
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
232
95505a9fa26f Uploaded
crs4
parents:
diff changeset
233 .. _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
234 .. _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
235 .. _MIT license: https://opensource.org/licenses/MIT
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
236
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
237 You can use this tool only if you agree to the license terms of: `Prokka`_.
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
238
13
a17498c603ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
iuc
parents: 12
diff changeset
239 .. _Prokka: http://github.com/tseemann/prokka
8
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
240 ]]></help>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
241 <citations>
392255fa7ab9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
parents: 7
diff changeset
242 <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
243 <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
244 </citations>
0
95505a9fa26f Uploaded
crs4
parents:
diff changeset
245 </tool>