Mercurial > repos > blankenberg > naive_variant_caller
changeset 9:4fab5fce1adb
Fix typo ("with with").
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Tue, 31 Mar 2015 11:11:15 -0400 |
| parents | d5f866df45ae |
| children | 907b40517289 |
| files | dependency_configs/tool_dependencies.xml tools/naive_variant_caller.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/dependency_configs/tool_dependencies.xml Thu Jan 29 15:02:01 2015 -0500 +++ b/dependency_configs/tool_dependencies.xml Tue Mar 31 11:11:15 2015 -0400 @@ -6,6 +6,6 @@ <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamparser_0_0_1" owner="blankenberg" changeset_revision="46bd908161b6" /> </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="102e3710dbdc" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamtools_0_0_1" owner="blankenberg" changeset_revision="9116288f9d4c" /> </package> </tool_dependency>
--- a/tools/naive_variant_caller.xml Thu Jan 29 15:02:01 2015 -0500 +++ b/tools/naive_variant_caller.xml Tue Mar 31 11:11:15 2015 -0400 @@ -93,7 +93,7 @@ <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" /> <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" /> - <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with with possible alternate alleles"/> + <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with possible alternate alleles"/> <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/> @@ -174,7 +174,7 @@ The number of genotype calls to make at each reported position. -Only write out positions with with possible alternate alleles: +Only write out positions with possible alternate alleles: When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.