| Previous changeset 12:23680a42e149 (2021-02-05) Next changeset 14:1d1762860d7e (2021-10-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572" |
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modified:
bcftools_view.xml |
| b |
| diff -r 23680a42e149 -r 98d5499ead46 bcftools_view.xml --- a/bcftools_view.xml Fri Feb 05 19:46:48 2021 +0000 +++ b/bcftools_view.xml Tue Apr 13 15:19:30 2021 +0000 |
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| @@ -38,7 +38,7 @@ #if str($section.max_ac) --max-ac ${section.max_ac} #end if -#if str($section.select_genotype) != "__none__": +#if str($section.select_genotype) != "None": --genotype "${section.select_genotype}" #end if ## known or novel @@ -121,13 +121,20 @@ help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" /> <param name="max_ac" type="integer" label="Max Ac" optional="True" help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" /> - <param name="select_genotype" type="select"> - <option value="__none__" selected="True">No selection</option> - <option value="require one or more hom/het/missing genotype or" /> - <option value="if prefixed with "^"" /> - <option value="exclude sites with hom/het/missing genotypes" /> + <param name="select_genotype" type="select" label="Select Genotype" optional="True"> + <help> + Include only sites with one or more homozygous (hom), heterozygous (het) or missing (miss) genotypes. + When prefixed with ^, the logic is reversed. + Please notice that if the input file doesn't have any genotype columns, + then this option is ignored altogether. + </help> + <option value="hom">hom</option> + <option value="het">het</option> + <option value="miss">miss</option> + <option value="^hom">^hom</option> + <option value="^het">^het</option> + <option value="^miss">^miss</option> </param> - <param name="types" type="select" label="Select Types" multiple="true" optional="True"> <help> List of variant types to select. Site is selected if any of the ALT alleles is of the type requested. @@ -345,6 +352,19 @@ </assert_contents> </output> </test> + <test> + <param name="input_file" ftype="vcf" value="view.vcf" /> + <param name="phased" value="--phased" /> + <param name="output_type" value="v" /> + <param name="select_genotype" value="^het" /> + <output name="output_file"> + <assert_contents> + <has_text text="--genotype ^het" /> + <has_text text="rs78249411" /> + <not_has_text text="3048719" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ ===================================== |