# HG changeset patch
# User dfornika
# Date 1572382408 14400
# Node ID 9378a784ce30a8975372c85bc8148cb05f5c08a8
# Parent  0f4abf21c415655c7eba8f61fae18770269d55fd
"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/prokka commit d0b060e7d9cc9fd89926dbc07fc93c8a1471b3fe-dirty"

diff -r 0f4abf21c415 -r 9378a784ce30 COPYING
--- a/COPYING	Tue Jul 09 12:31:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-Copyright © 2013 Lionel Guy
-Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/
-Copyright © 2015-2016 Earlham Institute http://earlham.ac.uk/
-Created by:
-Paolo Uva <paolo.uva@crs4.it>
-Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
-Lionel Guy <lionel.guy@icm.uu.se>
-Philip Mabon <philipmabon@gmail.com>
-
-Permission is hereby granted, free of charge, to any person obtaining a
-copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be included
-in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
-TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff -r 0f4abf21c415 -r 9378a784ce30 prokka.xml
--- a/prokka.xml	Tue Jul 09 12:31:34 2019 -0400
+++ b/prokka.xml	Tue Oct 29 16:53:28 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="prokka" name="Prokka" version="1.13">
+<tool id="prokka" name="Prokka" version="1.14">
     <description>Prokaryotic genome annotation</description>
     <requirements>
-        <requirement type="package" version="1.13">prokka</requirement>
+        <requirement type="package" version="1.14">prokka</requirement>
     </requirements>
 
     <version_command>prokka --version</version_command>
@@ -201,27 +201,6 @@
         </test>
     </tests>
     <help><![CDATA[
-**What it does**
-
-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.
-
-.. _Prokka: http://github.com/tseemann/prokka
-
-**Output files**
-
-Prokka creates several output files, which are described in the **Additional outputs** section above.
-
-**License and citation**
-
-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`_.
-
-.. _CRS4 Srl.: http://www.crs4.it/
-.. _Earlham Institute: http://earlham.ac.uk/
-.. _MIT license: https://opensource.org/licenses/MIT
-
-You can use this tool only if you agree to the license terms of: `Prokka`_.
-
-.. _Prokka: http://github.com/tseemann/prokka
     ]]></help>
     <citations>
         <citation type="doi">10.1093/bioinformatics/btu135</citation>
diff -r 0f4abf21c415 -r 9378a784ce30 readme.rst
--- a/readme.rst	Tue Jul 09 12:31:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-Prokka wrapper
-==============
-
-Warning
--------
-
-Prokka includes custom databases and is thus about a 340 MB download!
-
-Version history
----------------
-
-- Release 9 (prokka 1.12.0): Support Prokka 1.12. Uses updated conda dependency 1.12
-- Release 8 (prokka 1.11.1): Use Conda for installing tool dependencies, ToolShed dependencies are not supported anymore. Add a test. The tool is now maintained by the IUC.
-- Release 7 (prokka 1.11.0): 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.
-- Release 6 (prokka 1.4.0): 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>.
-- Release 5 (prokka 1.3.0): Fix Prokka 1.8 dependency installation.
-- Release 4 (prokka 1.3.0): Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 (requires Galaxy release_2013.11.04 or later). Update citation.
-- Release 3 (prokka 1.2.0): 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).
-- Release 2 (prokka 1.1.0): Merge the wrappers by CRS4 and Lionel Guy. Directly call prokka, remove prokka.py . Add 'locustag', 'increment', 'gffver', 'compliant', 'addgenes', 'genus', 'species', 'strain', 'plasmid', 'gcode', 'usegenus', 'metagenome', 'fast', 'evalue', 'norrna', 'notrna' params. Upgrade BLAST+ dependency to v. 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
-- Release 1 (prokka 1.0.1): Add txt output file. Use a definition list instead of a block quote in <help>. Correct 2 dependency minimum versions.
-- Release 0 (prokka 1.0.0): Initial release in the Tool Shed.
-
-Version history of (now deprecated) Lionel Guy's wrapper:
-
-- prokka 1.1.0: Merge the wrappers by CRS4 and Lionel Guy. Add COPYING file with MIT license. Make all params optional. Add 'gffver' param. Correctly quote text params in command. Use float type for 'evalue' param. Describe output files in help. Upgrade BLAST+ dependency to v. 2.2.28. Depend on package_aragorn_1_2_36 instead of trna_prediction. Depend on package_prodigal_2_60 instead of prodigal. Depend on package_barrnap_0_2 instead of barrnap. Add PROKKA_SITE_OPTIONS to env.sh and remove 'cpus' param.
-- prokka 0.2: Added this readme file. Support Prokka 1.7. Add dependencies management.
-- prokka 0.1: Initial release in the Tool Shed, supports Prokka 1.6.