Mercurial > repos > iuc > bcftools_convert_from_vcf
changeset 20:d58d2e8c7a57 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
| author | iuc |
|---|---|
| date | Tue, 16 Jul 2024 17:00:03 +0000 |
| parents | cacc9970727a |
| children | |
| files | bcftools_convert_from_vcf.xml macros.xml |
| diffstat | 2 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/bcftools_convert_from_vcf.xml Thu Jan 12 15:40:23 2023 +0000 +++ b/bcftools_convert_from_vcf.xml Tue Jul 16 17:00:03 2024 +0000 @@ -145,7 +145,7 @@ <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/> </outputs> <tests> - <test> + <test expect_num_outputs="2"> <param name="input_file" ftype="vcf" value="convert.vcf" /> <param name="convert_to" value="gen_sample" /> <output name="output_gen"> @@ -159,7 +159,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="2"> <param name="input_file" ftype="vcf" value="convert.vcf" /> <param name="convert_to" value="gen_sample" /> <param name="tag" value="GP" /> @@ -170,7 +170,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="2"> <param name="input_file" ftype="vcf" value="check.vcf" /> <param name="convert_to" value="gen_sample" /> <param name="tag" value="GT" /> @@ -182,7 +182,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="2"> <param name="input_file" ftype="vcf" value="convert.vcf" /> <param name="convert_to" value="hap_sample" /> <output name="output_hap"> @@ -191,7 +191,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="3"> <param name="input_file" ftype="vcf" value="convert.vcf" /> <param name="convert_to" value="hap_legend_sample" /> <output name="output_hap"> @@ -212,7 +212,7 @@ </output> </test> <!-- Test keep-duplicates option --> - <test> + <test expect_num_outputs="3"> <param name="input_file" ftype="vcf" value="convert.vcf" /> <param name="convert_to" value="hap_legend_sample" /> <param name="keep_duplicates" value="true"/> @@ -237,7 +237,7 @@ </assert_command> </test> <!-- Test region overlap --> - <test> + <test expect_num_outputs="2"> <param name="input_file" ftype="vcf" value="convert.vcf" /> <param name="convert_to" value="gen_sample" /> <section name="sec_restrict">
--- a/macros.xml Thu Jan 12 15:40:23 2023 +0000 +++ b/macros.xml Tue Jul 16 17:00:03 2024 +0000 @@ -174,7 +174,7 @@ </token> <xml name="macro_AF_file"> - <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" /> + <param argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" /> </xml> <!-- This may need to bgzip and tabix the file --> <token name="@PREPARE_AF_FILE@"> @@ -191,7 +191,7 @@ </token> <xml name="macro_estimate_AF"> - <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" /> + <param argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" /> </xml> <token name="@ESTIMATE_AF@"> #if 'estimate_AF' in $section and $section.estimate_AF: