Mercurial > repos > iuc > bcftools_gtcheck
changeset 2:025adf89e10d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6
| author | iuc |
|---|---|
| date | Mon, 03 Oct 2016 12:15:51 -0400 |
| parents | 247cc24f8b9e |
| children | bf8c3c146a1c |
| files | bcftools_gtcheck.xml macros.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/bcftools_gtcheck.xml Wed Jul 13 10:57:14 2016 -0400 +++ b/bcftools_gtcheck.xml Mon Oct 03 12:15:51 2016 -0400 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1"> <description>Check sample identity</description> <macros> <token name="@EXECUTABLE@">gtcheck</token> @@ -83,7 +83,7 @@ <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True" help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/> <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" /> - <param name="GTs_only" type="integer" label="Gts Only" default="99" optional="True" help="Use GTs, ignore PLs, using <int> for unseen genotypes" /> + <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using <int> for unseen genotypes" /> <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" /> <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" /> <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" /> @@ -96,6 +96,7 @@ <tests> <test> <param name="input_file" ftype="vcf" value="view.vcf" /> + <param name="GTs_only" value="" /> <output name="output_file"> <assert_contents> <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/>