Mercurial > repos > blankenberg > naive_variant_caller
changeset 12:ac0235d2d459 draft
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit ce964ed3ab7e390754fa03bb32a593fbe79dcf04
| author | blankenberg |
|---|---|
| date | Thu, 17 Sep 2015 14:56:15 -0400 |
| parents | 8af4e7a4d041 |
| children | cfc86c3fc5c8 |
| files | dependency_configs/tool_dependencies.xml tools/naive_variant_caller.py tools/naive_variant_caller.xml |
| diffstat | 3 files changed, 15 insertions(+), 13 deletions(-) [+] |
line wrap: on
line diff
--- 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>
--- 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 )
--- 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.