prokka: prokka.xml annotate

annotate prokka.xml @ 7:f5e44aad6498 draft

Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3.

author	crs4
date	Thu, 01 Oct 2015 14:14:06 -0400
parents	3ad7ef0ba385
children	392255fa7ab9

rev	line source
7 f5e44aad6498 Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3. crs4 parents: 6 diff changeset	1 <tool id="prokka" name="Prokka" version="1.11.0">
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	2 <description>prokaryotic genome annotation</description>
0 95505a9fa26f Uploaded crs4 parents: diff changeset	3 <requirements>
7 f5e44aad6498 Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3. crs4 parents: 6 diff changeset	4 <requirement type="package" version="2.2.31">blast+</requirement>
f5e44aad6498 Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3. crs4 parents: 6 diff changeset	5 <requirement type="package" version="3.1b2">hmmer</requirement>
0 95505a9fa26f Uploaded crs4 parents: diff changeset	6 <requirement type="package" version="1.2.36">aragorn</requirement>
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	7 <requirement type="package" version="2.60">prodigal</requirement>
7 f5e44aad6498 Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3. crs4 parents: 6 diff changeset	8 <requirement type="package" version="24.3">tbl2asn</requirement>
3 fffa1ae330ae Use $GALAXY_SLOTS instead of $PROKKA_SITE_OPTIONS. Upgrade Barrnap dependency to v. 0.3. Upgrade Infernal dependency to v. 1.1. Depend on package_gnu_parallel_20131122 (requires Galaxy release_2013.11.04 or later). crs4 parents: 2 diff changeset	9 <requirement type="package" version="20131122">gnu_parallel</requirement>
7 f5e44aad6498 Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3. crs4 parents: 6 diff changeset	10 <requirement type="package" version="0.7">barrnap</requirement>
3 fffa1ae330ae Use $GALAXY_SLOTS instead of $PROKKA_SITE_OPTIONS. Upgrade Barrnap dependency to v. 0.3. Upgrade Infernal dependency to v. 1.1. Depend on package_gnu_parallel_20131122 (requires Galaxy release_2013.11.04 or later). crs4 parents: 2 diff changeset	11 <requirement type="package" version="1.1">infernal</requirement>
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	12 <requirement type="package" version="0.1.6">minced</requirement>
7 f5e44aad6498 Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3. crs4 parents: 6 diff changeset	13 <requirement type="package" version="1.11">prokka</requirement>
0 95505a9fa26f Uploaded crs4 parents: diff changeset	14 </requirements>
95505a9fa26f Uploaded crs4 parents: diff changeset	15 <version_command>prokka --version</version_command>
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	16 <command>
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	17 prokka
3 fffa1ae330ae Use $GALAXY_SLOTS instead of $PROKKA_SITE_OPTIONS. Upgrade Barrnap dependency to v. 0.3. Upgrade Infernal dependency to v. 1.1. Depend on package_gnu_parallel_20131122 (requires Galaxy release_2013.11.04 or later). crs4 parents: 2 diff changeset	18 --cpus \${GALAXY_SLOTS:-8}
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	19 --quiet ## to avoid non-error messages written to stderr
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	20 --outdir outdir --prefix prokka ## used in outputs section
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	21 #if $locustag
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	22 --locustag "$locustag"
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	23 #end if
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	24 #if str($increment)
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 --increment $increment
0 95505a9fa26f Uploaded crs4 parents: diff changeset	26 #end if
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	27 --gffver $gffver
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	28 #if $compliant.compliant_select == "no"
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 #if $compliant.addgenes
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	30 --addgenes
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	31 #end if
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	32 #if str($compliant.mincontig)
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	33 --mincontig $compliant.mincontig
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	34 #end if
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	35 #else
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	36 --compliant
0 95505a9fa26f Uploaded crs4 parents: diff changeset	37 #end if
95505a9fa26f Uploaded crs4 parents: diff changeset	38 #if $centre
95505a9fa26f Uploaded crs4 parents: diff changeset	39 --centre "$centre"
95505a9fa26f Uploaded crs4 parents: diff changeset	40 #end if
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	41 #if $genus
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	42 --genus "$genus"
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	43 #end if
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	44 #if $species
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	45 --species "$species"
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	46 #end if
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	47 #if $strain
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	48 --strain "$strain"
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	49 #end if
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	50 #if $plasmid
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	51 --plasmid "$plasmid"
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	52 #end if
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	53 --kingdom $kingdom.kingdom_select
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	54 #if str($kingdom.gcode)
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	55 --gcode $kingdom.gcode
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	56 #end if
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	57 #if $usegenus
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	58 --usegenus
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	59 #end if
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	60 #if $proteins
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	61 --proteins $proteins
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	62 #end if
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	63 #if $metagenome
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	64 --metagenome
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	65 #end if
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	66 #if $fast
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	67 --fast
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	68 #end if
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	69 #if str($evalue)
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	70 --evalue $evalue
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	71 #end if
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	72 #if $rfam
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	73 --rfam
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	74 #end if
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	75 #if $norrna
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	76 --norrna
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	77 #end if
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	78 #if $notrna
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	79 --notrna
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	80 #end if
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	81 $input
0 95505a9fa26f Uploaded crs4 parents: diff changeset	82 </command>
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	83 <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
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	84 <stdio>
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	85 <exit_code range="1:" />
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	86 </stdio>
0 95505a9fa26f Uploaded crs4 parents: diff changeset	87 <inputs>
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	88 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
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	89 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
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	90 <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)">
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	91 <validator type="in_range" min="1" />
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	92 </param>
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	93 <param name="gffver" type="select" label="GFF version (--gffver)">
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	94 <option value="3">3</option>
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	95 <option value="2">2</option>
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	96 <option value="1">1</option>
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	97 </param>
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	98 <conditional name="compliant">
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	99 <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)">
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	100 <option value="no">No</option>
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	101 <option value="yes">Yes</option>
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	102 </param>
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	103 <when value="no">
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	104 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
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	105 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
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	106 </when>
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	107 <when value="yes" />
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	108 </conditional>
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	109 <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
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	110 <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
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	111 <param name="species" type="text" value="" label="Species name (--species)" />
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	112 <param name="strain" type="text" value="" label="Strain name (--strain)" />
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	113 <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
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	114 <conditional name="kingdom">
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	115 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
0 95505a9fa26f Uploaded crs4 parents: diff changeset	116 <option value="Archaea">Archaea</option>
95505a9fa26f Uploaded crs4 parents: diff changeset	117 <option value="Bacteria" selected="true">Bacteria</option>
95505a9fa26f Uploaded crs4 parents: diff changeset	118 <option value="Viruses">Viruses</option>
95505a9fa26f Uploaded crs4 parents: diff changeset	119 </param>
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	120 <when value="Archaea">
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	121 <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 -->
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	122 </when>
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	123 <when value="Bacteria">
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	124 <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 -->
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	125 <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
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	126 <option selected="true" value="none">N/A</option>
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	127 <option value="pos">positive</option>
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	128 <option value="neg">negative</option>
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	129 </param> SignalP is not FOSS -->
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	130 </when>
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	131 <when value="Viruses">
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	132 <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 -->
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	133 </when>
0 95505a9fa26f Uploaded crs4 parents: diff changeset	134 </conditional>
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	135 <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" />
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	136 <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
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	137 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
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	138 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
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	139 <param name="evalue" type="float" value="1e-06" optional="true" label="Similarity e-value cut-off">
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	140 <validator type="in_range" min="0" />
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	141 </param>
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	142 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" />
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	143 <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
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	144 <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
0 95505a9fa26f Uploaded crs4 parents: diff changeset	145 </inputs>
95505a9fa26f Uploaded crs4 parents: diff changeset	146 <outputs>
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	147 <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff" />
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	148 <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk" />
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	149 <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna" />
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	150 <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa" />
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	151 <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn" />
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	152 <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn" />
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	153 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa" />
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	154 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl" />
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	155 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err" />
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	156 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt" />
4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . crs4 parents: 1 diff changeset	157 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
0 95505a9fa26f Uploaded crs4 parents: diff changeset	158 </outputs>
95505a9fa26f Uploaded crs4 parents: diff changeset	159 <help>
95505a9fa26f Uploaded crs4 parents: diff changeset	160 What it does
95505a9fa26f Uploaded crs4 parents: diff changeset	161
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	162 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	163
95505a9fa26f Uploaded crs4 parents: diff changeset	164 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
95505a9fa26f Uploaded crs4 parents: diff changeset	165
95505a9fa26f Uploaded crs4 parents: diff changeset	166 Output files
95505a9fa26f Uploaded crs4 parents: diff changeset	167
1 4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	168 Prokka creates several output files:
0 95505a9fa26f Uploaded crs4 parents: diff changeset	169
1 4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	170 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	171 This is the master annotation in GFF format, containing both sequences and annotations
1 4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	172 gbk
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	173 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	174 fna
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	175 Nucleotide FASTA file of the input contig sequences
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	176 faa
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	177 Protein FASTA file of the translated CDS sequences
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	178 ffn
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	179 Nucleotide FASTA file of all the annotated sequences, not just CDS
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	180 sqn
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	181 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	182 fsa
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	183 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	184 tbl
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	185 Feature Table file, used by "tbl2asn" to create the .sqn file
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	186 err
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	187 Unacceptable annotations - the NCBI discrepancy report
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	188 log
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	189 Contains all the output that Prokka produced during its run
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	190 txt
4b6f16a79fe4 Add txt output file. crs4 parents: 0 diff changeset	191 Statistics relating to the annotated features found
0 95505a9fa26f Uploaded crs4 parents: diff changeset	192
95505a9fa26f Uploaded crs4 parents: diff changeset	193 License and citation
95505a9fa26f Uploaded crs4 parents: diff changeset	194
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	195 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_, © 2013 Lionel Guy and is released under the `MIT license`_.
0 95505a9fa26f Uploaded crs4 parents: diff changeset	196
95505a9fa26f Uploaded crs4 parents: diff changeset	197 .. _CRS4 Srl.: http://www.crs4.it/
95505a9fa26f Uploaded crs4 parents: diff changeset	198 .. _MIT license: http://opensource.org/licenses/MIT
95505a9fa26f Uploaded crs4 parents: diff changeset	199
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	200 You can use this tool only if you agree to the license terms of: `Prokka`_.
0 95505a9fa26f Uploaded crs4 parents: diff changeset	201
95505a9fa26f Uploaded crs4 parents: diff changeset	202 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
95505a9fa26f Uploaded crs4 parents: diff changeset	203 </help>
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	204 <citations>
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	205 <citation type="doi">10.1093/bioinformatics/btu135</citation>
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	206 <citation type="doi">10.1093/bioinformatics/btu153</citation>
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	207 </citations>
0 95505a9fa26f Uploaded crs4 parents: diff changeset	208 </tool>

Mercurial > repos > crs4 > prokka

annotate prokka.xml @ 7:f5e44aad6498 draft