| Previous changeset 4:13d534f2bcde (2013-09-16) Next changeset 6:55957494d4b1 (2014-02-05) |
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Commit message:
Update options. |
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modified:
dependency_configs/tool_dependencies.xml tools/naive_variant_caller.py tools/naive_variant_caller.xml |
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| diff -r 13d534f2bcde -r 8398666758e3 dependency_configs/tool_dependencies.xml --- a/dependency_configs/tool_dependencies.xml Mon Sep 16 10:41:15 2013 -0400 +++ b/dependency_configs/tool_dependencies.xml Tue Feb 04 17:26:26 2014 -0500 |
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| @@ -1,11 +1,11 @@ <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="74c21f9bdc39" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_numpy_1_7" owner="iuc" changeset_revision="ef12a3a11d5b" /> </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="ae1828dd8bbc" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamparser_0_0_1" owner="blankenberg" changeset_revision="0b2c2790838a" /> </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="de60d1631ce4" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamtools_0_0_1" owner="blankenberg" changeset_revision="b97259dc9149" /> </package> </tool_dependency> |
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| diff -r 13d534f2bcde -r 8398666758e3 tools/naive_variant_caller.py --- a/tools/naive_variant_caller.py Mon Sep 16 10:41:15 2013 -0400 +++ b/tools/naive_variant_caller.py Tue Feb 04 17:26:26 2014 -0500 |
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| @@ -18,8 +18,9 @@ parser.add_option( '-d', '--min_support_depth', dest='min_support_depth', action='store', type="int", default=0, help='Minimum number of reads needed to consider a REF/ALT. Default=0.' ) parser.add_option( '-q', '--min_base_quality', dest='min_base_quality', action='store', type="int", default=None, help='Minimum base quality.' ) parser.add_option( '-m', '--min_mapping_quality', dest='min_mapping_quality', action='store', type="int", default=None, help='Minimum mapping.' ) - parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default='uint8', help='dtype to use for coverage array' ) + parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default='uint64', help='dtype to use for coverage array' ) 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' ) (options, args) = parser.parse_args() @@ -55,8 +56,9 @@ regions.append( region ) coverage = VCFReadGroupGenotyper( map( lambda x: Reader( *x ), bam_files ), options.reference_genome_filename, dtype=options.coverage_dtype, - min_support_depth=options.min_support_depth, min_base_quality=options.min_base_quality, min_mapping_quality=options.min_mapping_quality, - restrict_regions=regions, use_strand=options.use_strand, allow_out_of_bounds_positions=options.allow_out_of_bounds_positions ) + min_support_depth=options.min_support_depth, min_base_quality=options.min_base_quality, + min_mapping_quality=options.min_mapping_quality, restrict_regions=regions, use_strand=options.use_strand, + allow_out_of_bounds_positions=options.allow_out_of_bounds_positions, safe=options.safe ) for line in coverage.iter_vcf( ploidy=options.ploidy, variants_only=options.variants_only ): out.write( "%s\n" % line ) out.close() |
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| diff -r 13d534f2bcde -r 8398666758e3 tools/naive_variant_caller.xml --- a/tools/naive_variant_caller.xml Mon Sep 16 10:41:15 2013 -0400 +++ b/tools/naive_variant_caller.xml Tue Feb 04 17:26:26 2014 -0500 |
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| @@ -43,10 +43,14 @@ --min_mapping_quality "${min_mapping_quality}" #end if - --coverage_dtype "${coverage_dtype}" - --allow_out_of_bounds_positions + #if str( $advanced_options.advanced_options_selector ) == "advanced": + --coverage_dtype "${advanced_options.coverage_dtype}" + ${advanced_options.safe} + #else + --coverage_dtype "uint64" + #end if </command> <inputs> <conditional name="reference_source"> @@ -93,12 +97,24 @@ <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/> - <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM"> - <option value="uint8">uint8</option> - <option value="uint16" selected="True">uint16</option> - <option value="uint32">uint32</option> - <option value="uint64">uint64</option> - </param> + <conditional name="advanced_options"> + <param name="advanced_options_selector" type="select" label="Show Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic"> + <!-- Do nothing here --> + </when> + <when value="advanced"> + <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM"> + <option value="uint8">uint8</option> + <option value="uint16">uint16</option> + <option value="uint32">uint32</option> + <option value="uint64" selected="True">uint64</option> + </param> + <param name="safe" type="boolean" truevalue="--safe" falsevalue="" checked="False" label="Be extra safe"/> + </when> + </conditional> </inputs> <outputs> @@ -200,6 +216,7 @@ <param name="ploidy" value="2" /> <param name="variants_only" value="False" /> <param name="use_strand" value="False" /> + <param name="advanced_options_selector" value="advanced" /> <param name="coverage_dtype" value="uint8" /> <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" /> </test> |