Mercurial > repos > iuc > bcftools_stats
changeset 20:bf8325a07ce7 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 17:04:38 +0000 |
| parents | a2f8dc22d7c0 |
| children | |
| files | bcftools_stats.xml macros.xml |
| diffstat | 2 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/bcftools_stats.xml Thu Jan 12 15:33:09 2023 +0000 +++ b/bcftools_stats.xml Tue Jul 16 17:04:38 2024 +0000 @@ -157,13 +157,13 @@ </param> </inputs> <outputs> - <data name="output_file" format="txt"/> - <data name="output_pdf" format="pdf" from_work_dir="plot_tmp/summary.pdf"> + <data name="output_file" format="txt" label="${tool.name} on ${on_string}: txt" /> + <data name="output_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF" from_work_dir="plot_tmp/summary.pdf"> <filter>plot_title</filter> </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="input_file" ftype="vcf" value="stats.b.vcf" /> <param name="inputB_file" ftype="vcf" value="stats.a.vcf" /> <output name="output_file"> @@ -173,7 +173,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="1"> <param name="input_file" ftype="vcf" value="mpileup.vcf" /> <section name="sec_default"> <expand macro="test_using_reference" select_from="cached" ref="mpileup" /> @@ -186,7 +186,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="2"> <param name="input_file" ftype="vcf" value="mpileup.vcf" /> <param name="plot_title" value="Plot for mpileup.vcf" /> <output name="output_file"> @@ -199,7 +199,7 @@ <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" /> </test> <!-- Test region overlap option--> - <test> + <test expect_num_outputs="1"> <param name="input_file" ftype="vcf" value="stats.b.vcf" /> <param name="inputB_file" ftype="vcf" value="stats.a.vcf" /> <section name="sec_restrict"> @@ -216,7 +216,7 @@ </assert_command> </test> <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605 - <test> + <test expect_num_outputs="1"> <param name="input_file" value="mpileup.vcf.gz" /> <output name="output_file"> <assert_contents> @@ -228,7 +228,7 @@ </test> --> <!-- Test modification in samples option --> - <test> + <test expect_num_outputs="1"> <param name="input_file" ftype="vcf" value="mpileup.vcf" /> <section name="sec_restrict"> <param name="samples" value="-" />
--- a/macros.xml Thu Jan 12 15:33:09 2023 +0000 +++ b/macros.xml Tue Jul 16 17:04:38 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: