# HG changeset patch
# User crs4
# Date 1414406752 14400
# Node ID 3ad7ef0ba385b9a764cb677493b19f012b268225
# Parent  b9fea998270aa73d56b330de13f808d4df8d1a6f
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>.

diff -r b9fea998270a -r 3ad7ef0ba385 COPYING
--- a/COPYING	Thu Jan 09 16:49:50 2014 -0500
+++ b/COPYING	Mon Oct 27 06:45:52 2014 -0400
@@ -4,6 +4,7 @@
 Paolo Uva <paolo.uva@crs4.it>
 Nicola Soranzo <nicola.soranzo@crs4.it>
 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
diff -r b9fea998270a -r 3ad7ef0ba385 prokka.xml
--- a/prokka.xml	Thu Jan 09 16:49:50 2014 -0500
+++ b/prokka.xml	Mon Oct 27 06:45:52 2014 -0400
@@ -1,16 +1,16 @@
-<tool id="prokka" name="Prokka" version="1.3.0">
+<tool id="prokka" name="Prokka" version="1.4.0">
   <description>prokaryotic genome annotation</description>
   <requirements>
     <requirement type="package" version="2.2.28">blast+</requirement>
     <requirement type="package" version="3.1b1">hmmer</requirement>
     <requirement type="package" version="1.2.36">aragorn</requirement>
     <requirement type="package" version="2.60">prodigal</requirement>
-    <requirement type="package" version="22.4">tbl2asn</requirement>
+    <requirement type="package" version="23.7">tbl2asn</requirement>
     <requirement type="package" version="20131122">gnu_parallel</requirement>
-    <requirement type="package" version="0.3">barrnap</requirement>
+    <requirement type="package" version="0.5">barrnap</requirement>
     <requirement type="package" version="1.1">infernal</requirement>
-    <requirement type="package" version="0.1.4">minced</requirement>
-    <requirement type="package" version="1.8">prokka</requirement>
+    <requirement type="package" version="0.1.6">minced</requirement>
+    <requirement type="package" version="1.10">prokka</requirement>
   </requirements>
   <version_command>prokka --version</version_command>
   <command>
@@ -57,6 +57,9 @@
     #if $usegenus
       --usegenus
     #end if
+    #if $proteins
+      --proteins $proteins
+    #end if
     #if $metagenome
       --metagenome
     #end if
@@ -77,9 +80,13 @@
     #end if
     $input
   </command>
+  <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
   <inputs>
     <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
-    <param name="locustag" type="text" value="PROKKA" optional="true" label="Locus tag prefix (--locustag)" />
+    <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
     <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)">
       <validator type="in_range" min="1" />
     </param>
@@ -99,11 +106,11 @@
       </when>
       <when value="yes" />
     </conditional>
-    <param name="centre" type="text" value="" optional="true" label="Sequencing centre ID (--centre)" />
-    <param name="genus" type="text" value="" optional="true" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
-    <param name="species" type="text" value="" optional="true" label="Species name (--species)" />
-    <param name="strain" type="text" value="" optional="true" label="Strain name (--strain)" />
-    <param name="plasmid" type="text" value="" optional="true" label="Plasmid name or identifier (--plasmid)" />
+    <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
+    <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
+    <param name="species" type="text" value="" label="Species name (--species)" />
+    <param name="strain" type="text" value="" label="Strain name (--strain)" />
+    <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
     <conditional name="kingdom">
       <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
         <option value="Archaea">Archaea</option>
@@ -126,6 +133,7 @@
       </when>
     </conditional>
     <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" />
+    <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
     <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
     <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
     <param name="evalue" type="float" value="1e-06" optional="true" label="Similarity e-value cut-off">
@@ -184,18 +192,27 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_, Lionel Guy and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_, © 2013 Lionel Guy and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
 .. _MIT license: http://opensource.org/licenses/MIT
 
-If you use this tool in Galaxy, please cite |Cuccuru2013|_.
-
-.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
-.. _Cuccuru2013: http://orione.crs4.it/
-
-This tool uses `Prokka`_, which is licensed separately. Please cite Seemann, T. (2013) Prokka: Rapid Prokaryotic Genome Annotation. *Submitted*
+You can use this tool only if you agree to the license terms of: `Prokka`_.
 
 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
+
+If you use this tool, please cite:
+
+- |Cuccuru2014|_
+- |Seemann2014|_.
+
+.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
+.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
+.. |Seemann2014| replace:: Seemann, T. (2014) Prokka: rapid prokaryotic genome annotation. *Bioinformatics* 30(14), 2068-2069
+.. _Seemann2014: http://bioinformatics.oxfordjournals.org/content/30/14/2068
   </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btu135</citation>
+    <citation type="doi">10.1093/bioinformatics/btu153</citation>
+  </citations>
 </tool>
diff -r b9fea998270a -r 3ad7ef0ba385 readme.rst
--- a/readme.rst	Thu Jan 09 16:49:50 2014 -0500
+++ b/readme.rst	Mon Oct 27 06:45:52 2014 -0400
@@ -4,9 +4,9 @@
 Warning
 -------
 
-Prokka includes custom databases and is thus about a 2.0 GB download!
+Prokka includes custom databases and is thus about a 340 MB download!
 
-Dependencies of Prokka which needs to be installed separately
+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;
@@ -20,7 +20,7 @@
 Configuration
 -------------
 
-prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see http://wiki.galaxyproject.org/Admin/Config/Jobs and http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
+prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
 
 If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool.
 
@@ -30,11 +30,12 @@
 
 (where N is the number of CPU cores allocated by the job runner for this tool) to the file
 
-  <tool_dependencies_dir>/prokka/1.7/crs4/prokka/<hash_string>/env.sh
+  <tool_dependencies_dir>/prokka/1.10/crs4/prokka/<hash_string>/env.sh
 
 Version history
 ---------------
 
+- 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).
diff -r b9fea998270a -r 3ad7ef0ba385 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jan 09 16:49:50 2014 -0500
+++ b/tool_dependencies.xml	Mon Oct 27 06:45:52 2014 -0400
@@ -1,37 +1,37 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="blast+" version="2.2.28">
-    <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="hmmer" version="3.1b1">
-    <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="aragorn" version="1.2.36">
-    <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="prodigal" version="2.60">
-    <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="tbl2asn" version="22.4">
-    <repository changeset_revision="55f52e5395cd" name="package_tbl2asn_22_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  <package name="tbl2asn" version="23.7">
+    <repository changeset_revision="2271d52a8531" name="package_tbl2asn_23_7" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="gnu_parallel" version="20131122">
-    <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="barrnap" version="0.3">
-    <repository changeset_revision="60763b9e2026" name="package_barrnap_0_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  <package name="barrnap" version="0.5">
+    <repository changeset_revision="ec528d56b01f" name="package_barrnap_0_5" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="infernal" version="1.1">
-    <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="minced" version="0.1.4">
-    <repository changeset_revision="0cf9719bfe4b" name="package_minced_0_1_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  <package name="minced" version="0.1.6">
+    <repository changeset_revision="a135862cd007" name="package_minced_0_1_6" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="prokka" version="1.8">
+  <package name="prokka" version="1.10">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
-        <action target_filename="bin/prokka" type="download_file">http://www.vicbioinformatics.com/prokka-1.8</action>
+        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.10.tar.gz</action>
+        <action type="shell_command">bin/prokka --setupdb</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
           <destination_directory>$INSTALL_DIR</destination_directory>
@@ -42,7 +42,7 @@
       </actions>
     </install>
     <readme>
-Warning: Prokka includes custom databases and is thus about a 2.0 GB download!
+Warning: Prokka includes custom databases and is thus about a 340 MB download!
 
 Dependencies of Prokka which needs to be installed separately:
 - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;