# HG changeset patch
# User blankenberg
# Date 1442516175 14400
# Node ID ac0235d2d45956af74927dc4282287ec06aaf79b
# Parent  8af4e7a4d04139f58f7b603943c3ffe4620804c4
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit ce964ed3ab7e390754fa03bb32a593fbe79dcf04

diff -r 8af4e7a4d041 -r ac0235d2d459 dependency_configs/tool_dependencies.xml
--- a/dependency_configs/tool_dependencies.xml	Thu Sep 17 14:22:52 2015 -0400
+++ b/dependency_configs/tool_dependencies.xml	Thu Sep 17 14:56:15 2015 -0400
@@ -1,11 +1,12 @@
+<?xml version="1.0"?>
 <tool_dependency>
     <package name="numpy" version="1.7.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_numpy_1_7" owner="iuc" changeset_revision="ef12a3a11d5b" />
+        <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="pyBamParser" version="0.0.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamparser_0_0_1" owner="blankenberg" changeset_revision="46bd908161b6" />
+        <repository changeset_revision="a0fb4b5a1679" name="package_pybamparser_0_0_1" owner="blankenberg" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="pyBamTools" version="0.0.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamtools_0_0_1" owner="blankenberg" changeset_revision="9116288f9d4c" />
+    <package name="pyBamTools" version="0.0.2">
+        <repository changeset_revision="38fc6b348c17" name="package_pybamtools_0_0_2" owner="blankenberg" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r 8af4e7a4d041 -r ac0235d2d459 tools/naive_variant_caller.py
--- a/tools/naive_variant_caller.py	Thu Sep 17 14:22:52 2015 -0400
+++ b/tools/naive_variant_caller.py	Thu Sep 17 14:56:15 2015 -0400
@@ -1,9 +1,10 @@
+#!/usr/bin/env python
 #Dan Blankenberg
 import sys
 import optparse
 
 from pyBamParser.bam import Reader
-from pyBamTools.genotyping.naive import VCFReadGroupGenotyper
+from pyBamTools.genotyping.naive import VCFReadGroupGenotyper, PROGRAM_NAME, PROGRAM_VERSION
 
 def main():
     #Parse Command Line
@@ -22,8 +23,13 @@
     parser.add_option( '--allow_out_of_bounds_positions', dest='allow_out_of_bounds_positions', action='store_true', default = False, help='Allows out of bounds positions to not throw fatal errors' )
     parser.add_option( '--safe', dest='safe', action='store_true', default = False, help='Perform checks to prevent certain errors. Is slower.' )
     parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' )
+    parser.add_option( '', '--version', dest='version', action='store_true', default = False, help='Report version and quit' )
     (options, args) = parser.parse_args()
     
+    if options.version:
+        print "%s version %s" % ( PROGRAM_NAME, PROGRAM_VERSION )
+        sys.exit(0)
+    
     if len( options.bam_file ) == 0:
         print >>sys.stderr, 'You must provide at least one bam (-b) file.'
         parser.print_help( sys.stderr )
diff -r 8af4e7a4d041 -r ac0235d2d459 tools/naive_variant_caller.xml
--- a/tools/naive_variant_caller.xml	Thu Sep 17 14:22:52 2015 -0400
+++ b/tools/naive_variant_caller.xml	Thu Sep 17 14:56:15 2015 -0400
@@ -1,9 +1,9 @@
-<tool id="naive_variant_caller" name="Naive Variant Caller" version="0.0.1">
+<tool id="naive_variant_caller" name="Naive Variant Caller" version="0.0.2">
   <description> - tabulate variable sites from BAM datasets</description>
   <requirements>
     <requirement type="package" version="1.7.1">numpy</requirement>
     <requirement type="package" version="0.0.1">pyBamParser</requirement>
-    <requirement type="package" version="0.0.1">pyBamTools</requirement>
+    <requirement type="package" version="0.0.2">pyBamTools</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" err_level="fatal" />
@@ -52,6 +52,7 @@
          ${advanced_options.safe}
      #end if 
   </command>
+  <version_command interpreter="python">naive_variant_caller.py --version</version_command>
   <inputs>
     <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
@@ -122,12 +123,6 @@
     <data format="vcf" name="output_vcf" />
   </outputs>
   <help>
-.. class:: warningmark
-
-Upgrading to version 0.0.2 is recommended.
-
-------
-
 **What it does**
 
 This tool is a naive variant caller that processes aligned sequencing reads from the BAM format and produces a VCF file containing per position variant calls. This tool allows multiple BAM files to be provided as input and utilizes read group information to make calls for individual samples.