Mercurial > repos > iuc > bcftools_consensus
changeset 21:1171446da5db 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 17:12:58 +0000 |
| parents | 147de996e34f |
| children | |
| files | bcftools_consensus.xml macros.xml |
| diffstat | 2 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- a/bcftools_consensus.xml Thu Jan 12 15:42:32 2023 +0000 +++ b/bcftools_consensus.xml Tue Jul 16 17:12:58 2024 +0000 @@ -139,7 +139,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="2"> <expand macro="test_using_reference" ref="consensus.fa" /> <param name="input_file" ftype="vcf" value="consensus.vcf" /> <param name="mask" ftype="tabular" value="consensus.tab" /> @@ -155,7 +155,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="2"> <expand macro="test_using_reference" select_from="cached" ref="consensus" /> <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" /> <param name="mask" ftype="tabular" value="consensus.tab" /> @@ -171,7 +171,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="1"> <expand macro="test_using_reference" ref="consensus.fa" /> <param name="input_file" ftype="vcf" value="consensus.vcf" /> <param name="mask" ftype="tabular" value="consensus.tab" /> @@ -186,7 +186,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="1"> <expand macro="test_using_reference" ref="consensus.fa" /> <param name="input_file" ftype="vcf" value="consensus.vcf" /> <section name="sec_restrict"> @@ -199,7 +199,7 @@ </output> </test> <!--Test absent option--> - <test> + <test expect_num_outputs="1"> <expand macro="test_using_reference" ref="consensus.fa" /> <param name="input_file" ftype="vcf" value="consensus.vcf" /> <section name="sec_restrict"> @@ -216,7 +216,7 @@ </assert_command> </test> <!--Test mask options --> - <test> + <test expect_num_outputs="1"> <expand macro="test_using_reference" ref="consensus.fa" /> <param name="input_file" ftype="vcf" value="consensus.vcf" /> <section name="sec_restrict">
--- a/macros.xml Thu Jan 12 15:42:32 2023 +0000 +++ b/macros.xml Tue Jul 16 17:12:58 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: