# HG changeset patch
# User iuc
# Date 1477747749 14400
# Node ID fd4b2f03cfc690ab03541b1c702b61108dfa5eca
# Parent  6aa88a432ffc819490103f8ad12840e36cd78f07
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8

diff -r 6aa88a432ffc -r fd4b2f03cfc6 prokka.xml
--- a/prokka.xml	Sat Oct 29 09:15:32 2016 -0400
+++ b/prokka.xml	Sat Oct 29 09:29:09 2016 -0400
@@ -130,17 +130,17 @@
         <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
         <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
 
-        <param name="outputs" type="select" multiple="true" label="Additional outputs">
-            <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations</option>
-            <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence</option>
-            <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences</option>
-            <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences</option>
-            <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS</option>
-            <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.</option>
-            <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines</option>
-            <option value="tbl" selected="True">Feature Table file</option>
-            <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report</option>
-            <option value="txt" selected="True">Statistics relating to the annotated features found</option>
+        <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
+            <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option>
+            <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>
+            <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option>
+            <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option>
+            <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option>
+            <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>
+            <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines (.fsa)</option>
+            <option value="tbl" selected="True">Feature Table file (.tbl)</option>
+            <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option>
+            <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option>
         </param>
 
     </inputs>
@@ -207,30 +207,7 @@
 
 **Output files**
 
-Prokka creates several output files:
-
-gff
-    This is the master annotation in GFF format, containing both sequences and annotations
-gbk
-    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
-fna
-    Nucleotide FASTA file of the input contig sequences
-faa
-    Protein FASTA file of the translated CDS sequences
-ffn
-    Nucleotide FASTA file of all the annotated sequences, not just CDS
-sqn
-    An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.
-fsa
-    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
-tbl
-    Feature Table file, used by "tbl2asn" to create the .sqn file
-err
-    Unacceptable annotations - the NCBI discrepancy report
-log
-    Contains all the output that Prokka produced during its run
-txt
-    Statistics relating to the annotated features found
+Prokka creates several output files, which are described in the **Additional outputs** section above.
 
 **License and citation**
 
diff -r 6aa88a432ffc -r fd4b2f03cfc6 readme.rst
--- a/readme.rst	Sat Oct 29 09:15:32 2016 -0400
+++ b/readme.rst	Sat Oct 29 09:29:09 2016 -0400
@@ -6,20 +6,10 @@
 
 Prokka includes custom databases and is thus about a 340 MB download!
 
-Dependencies of Prokka which need to be installed separately
--------------------------------------------------------------
-
-- Perl core modules: File\::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
-- Perl modules: Bio::SeqIO from BioPerl_ >= 1.6.900, `XML::Simple`_;
-- SignalP_ >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, it is not used in the tool wrapper.
-
-.. _BioPerl: http://search.cpan.org/dist/BioPerl/
-.. _XML::Simple: http://search.cpan.org/dist/XML-Simple/
-.. _SignalP: http://www.cbs.dtu.dk/services/SignalP/
-
 Version history
 ---------------
 
+- 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.