# HG changeset patch
# User lionelguy
# Date 1378308793 14400
# Node ID 2bb7c28ea68ff201db01e108b2327a0677afe01c
# Parent  5c0b71c6a2b0102604a100225070e9d853ea44cd
Committed version 0.2: added dependency management and a readme file, and support prokka 1.7

diff -r 5c0b71c6a2b0 -r 2bb7c28ea68f prokka.xml
--- a/prokka.xml	Tue Sep 03 10:15:54 2013 -0400
+++ b/prokka.xml	Wed Sep 04 11:33:13 2013 -0400
@@ -1,14 +1,14 @@
-<tool id="prokka" name="prokka" version="0.1">
+<tool id="prokka" name="prokka" version="0.2">
   <description>prokaryotic genome annotation</description>
   <requirements>
-    <requirement type="package" version="1.6">prokka</requirement>
+    <requirement type="package" version="1.7">prokka</requirement>
     <requirement type="package" version="1.2.36">aragorn</requirement>
-    <requirement type="package" version="1.2">rnammer</requirement>
     <requirement type="package" version="2.60">prodigal</requirement>
-    <requirement type="package" version="4.1">signalp</requirement>
-    <requirement type="package" version="3.0">infernal</requirement>
-    <requirement type="package" version="3.1">hmmer</requirement>
-    <requirement type="package">blast+</requirement>
+    <requirement type="package" version="0.1">barrnap</requirement>
+    <!-- <requirement type="package" version="4.1">signalp</requirement> -->
+    <!-- <requirement type="package" version="3.0">infernal</requirement> -->
+    <requirement type="package" version="3.1b1">hmmer</requirement>
+    <requirement type="package" version="2.2.26+">blast+</requirement>
     <requirement type="package">tbl2asn</requirement>
   </requirements>
   <version_command>prokka --version</version_command>
@@ -17,12 +17,26 @@
   --prefix prokka
   $addgenes
   --locustag $locustag
+  $compliant
   --increment $increment
+  #if str($centre) != ""
   --centre $centre
-  --genus $genus --species $species --strain $strain
+  #end if
+  #if str($genus) != ""
+  --genus $genus 
+  #end if 
+  #if str($species) != ""
+  --species $species 
+  #end if 
+  #if str($strain) != ""
+  --strain $strain 
+  #end if 
+  #if str($plasmid) != ""
+  --plasmid $plasmid
+  #end if 
   --kingdom $kingdom
   --gcode $gcode
-  #if $gram != "none"
+  #if $gram != "None"
   --gram $gram
   #end if
   $usegenus
@@ -31,6 +45,9 @@
   --cpus $cpus
   --mincontig $mincontig
   --evalue $evalue
+  $rfam
+  $norrna
+  $notrna
   $input
   </command>
   <inputs>
@@ -38,10 +55,12 @@
     <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix"/>
     <param name="addgenes" type="boolean" truevalue="--addgenes" falsevalue="" checked="false" label="Add 'gene' features for each 'CDS' feature" />
     <param name="increment" type="integer" value="10" label="Locus tag counter increment" />
-    <param name="centre" type="text" value="molevoUU" label="Locus tag prefix"/>
+    <param name="compliant" type="boolean" truevalue="--compliant" falsevalue="" checked="false" label="Force Genbank/ENA/DDJB compliance: --genes --mincontiglen 200 --centre XXX" />
+    <param name="centre" type="text" value="XXX" label="Locus tag prefix"/>
     <param name="genus" type="text" value="Genus" label="Genus name (will be used to aid annotation)"/>
     <param name="species" type="text" value="species" label="Species name"/>
     <param name="strain" type="text" value="strain" label="Strain name"/>
+    <param name="plasmid" type="text" value="" label="Plasmid name or identifier"/>
     <param name="kingdom" type="select" display="radio" label="Annotation mode">
       <option value="Archaea">Archaea</option>
       <option value="Bacteria" selected="True">Bacteria</option>
@@ -60,6 +79,8 @@
     <param name="mincontig" type="integer" value="200" label="Minimum contig size [NCBI needs 200]" />
     <param name="evalue" type="text" value="1e-06" label="Similarity e-value cut-off" />
     <param name="rfam" type="boolean" truevalue="--rfam" falsevalue="" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
+    <param name="norrna" type="boolean" truevalue="--norrna" falsevalue="" checked="false" label="Don't run rRNA search" />
+    <param name="notrna" type="boolean" truevalue="--notrna" falsevalue="" checked="false" label="Don't run tRNA search" />
   </inputs>
   <outputs>
     <data name="out_gff" format="gff" label="GFF" from_work_dir="outdir/prokka.gff"/>
@@ -74,8 +95,13 @@
     <data name="out_err" format="txt" label="Errors" from_work_dir="outdir/prokka.err"/>
   </outputs>
   <stdio>
-    <exit_code range="1:" level="fatal" description="Error" />
-  </stdio>  
+    <!--<exit_code range="1:" level="fatal" description="Error" />-->
+    <regex match="not a readable non-empty FASTA file"
+	   source="stdout"
+	   level="fatal"
+	   description="Input file not a readable non-empty FASTA file" />
+  </stdio> 
+  
   <help>
 **What it does**
 
diff -r 5c0b71c6a2b0 -r 2bb7c28ea68f readme.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Wed Sep 04 11:33:13 2013 -0400
@@ -0,0 +1,35 @@
+Prokka wrapper
+==============
+
+Warning
+-------
+
+Prokka comes with custom databases and is thus very large: **~2Gb**!
+
+Note
+----
+
+- **infernal** >= 1.1rc4 is an optional dependency to find non-coding RNAs. An executable is shipped with prokka.
+- **SignalP** >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, no automatic dependency is managed.
+- **tbl2asn** >= 21.0 is required. This dependency is not managed here. The reason is that versions are increasing very rapidly. The software can be downloaded from the NCBI (ftp) at the following address.
+ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/
+- **BioPerl** >= 1.6 is required, but the dependency is not managed here, although it might in future. 
+- **GNU Parallel** >= 20120322 is required but is shipped with Prokka and thus is not managed by the tool dependency system
+
+Version history
+---------------
+
+- v0.2: added this readme file, supports prokka 1.7 and adds dependencies management.
+- v0.1: initial release in the toolshed, supports prokka 1.6.
+
+
+Copyright
+---------
+
+prokka is developed by  Torsten Seemann at Victorian Bioinformatics Consortium http://www.bioinformatics.net.au/. prokka is released under GPLv3 or later.
+
+This wrapper is copyrighted by Lionel Guy, and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
diff -r 5c0b71c6a2b0 -r 2bb7c28ea68f repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Wed Sep 04 11:33:13 2013 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<repositories description="Prokka requires a suite of other tools">
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="trna_prediction" owner="bgruening" changeset_revision="d34f31cbc9dd" />
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="barrnap" owner="simon-gladman" changeset_revision="a41418a3bd38" />
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="prodigal" owner="edward-kirton" changeset_revision="304c1a67bb7b" />
+  <!--<repository toolshed="http://toolshed.g2.bx.psu.edu" name="infernal" owner="" changeset_revision="" /> -->
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_hmmer_3_1 " owner="lionelguy" changeset_revision="007c736bf7e8" />
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast+" owner="devteam" changeset_revision="9dabbfd73c8a" />
+</repositories>
\ No newline at end of file
diff -r 5c0b71c6a2b0 -r 2bb7c28ea68f tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 04 11:33:13 2013 -0400
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="prokka" version="1.7">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
+                <!-- Copying the whole bin, binaries, doc and db folders -->
+		<action type="make_directory">$INSTALL_DIR/bin</action>
+		<action type="make_directory">$INSTALL_DIR/binaries</action>
+		<action type="make_directory">$INSTALL_DIR/db</action>
+		<action type="make_directory">$INSTALL_DIR/doc</action>
+		<action type="move_directory_files">
+		  <source_directory>bin</source_directory>
+		  <destination_directory>$INSTALL_DIR/bin</destination_directory>
+		</action>
+                <action type="move_directory_files">
+		  <source_directory>binaries</source_directory>
+		  <destination_directory>$INSTALL_DIR/binaries</destination_directory>
+		</action>
+                <action type="move_directory_files">
+		  <source_directory>db</source_directory>
+		  <destination_directory>$INSTALL_DIR/db</destination_directory>
+		</action>
+                <action type="move_directory_files">
+		  <source_directory>doc</source_directory>
+		  <destination_directory>$INSTALL_DIR/doc</destination_directory>
+		</action>
+                <action type="set_environment">
+		  <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+    
+    <readme>
+This installs prokka 1.7
+Note: this is about a 2.0 GB download due to included custom databases.</readme>
+  </package>
+</tool_dependency>