| Previous changeset 1:247cc24f8b9e (2016-07-13) Next changeset 3:bf8c3c146a1c (2017-01-31) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6 |
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modified:
bcftools_gtcheck.xml macros.xml |
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| diff -r 247cc24f8b9e -r 025adf89e10d bcftools_gtcheck.xml --- a/bcftools_gtcheck.xml Wed Jul 13 10:57:14 2016 -0400 +++ b/bcftools_gtcheck.xml Mon Oct 03 12:15:51 2016 -0400 |
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| @@ -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"/> |
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| diff -r 247cc24f8b9e -r 025adf89e10d macros.xml --- a/macros.xml Wed Jul 13 10:57:14 2016 -0400 +++ b/macros.xml Mon Oct 03 12:15:51 2016 -0400 |
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| @@ -339,7 +339,6 @@ </when> <when value="targets_file"> <expand macro="macro_targets_file"> - <optional>true</optional> </expand> </when> </conditional> |