Mercurial > repos > iuc > bcftools_query
diff bcftools_query.xml @ 25:eea8a0f18b24 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
| author | iuc |
|---|---|
| date | Tue, 02 Dec 2025 07:42:36 +0000 |
| parents | 7106fdae4823 |
| children |
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--- a/bcftools_query.xml Sun Aug 18 09:41:23 2024 +0000 +++ b/bcftools_query.xml Tue Dec 02 07:42:36 2025 +0000 @@ -8,7 +8,6 @@ <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ -@PREPARE_ENV@ @PREPARE_INPUT_FILES@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ @@ -43,8 +42,8 @@ <section name="sec_restrict" expanded="false" title="Restrict to"> <expand macro="macro_collapse" /> <expand macro="macro_samples" /> - <expand macro="macro_restrict" /> - <expand macro="macro_restrict" type="target" label_type="Target" /> + <expand macro="macro_region_restrict" /> + <expand macro="macro_target_restrict" /> <expand macro="macro_include" /> <expand macro="macro_exclude" /> </section> @@ -77,19 +76,28 @@ <tests> <test> <param name="input_files" ftype="vcf" value="query.vcf" /> - <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> - <param name="tsv" value="True" /> + <section name="sec_query"> + <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> + <param name="tsv" value="True" /> + </section> <output name="output_file" file="query.out" /> </test> <!-- Test region overlap option--> <test> <param name="input_files" ftype="vcf" value="query.vcf" /> - <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> - <param name="tsv" value="True" /> + <section name="sec_query"> + <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> + <param name="tsv" value="True" /> + </section> <section name="sec_restrict"> - <param name="regions_overlap" value="1"/> + <conditional name="regions"> + <param name="regions_src" value="regions" /> + <repeat name="region_specs"> + <param name="chrom" value="1" /> + </repeat> + </conditional> </section> - <output name="output_file" file="query.out" /> + <output name="output_file" file="query.out" compare="contains" lines_diff="4"/> <assert_command> <has_text text="--regions-overlap" /> </assert_command> @@ -150,7 +158,7 @@ @BCFTOOLS_MANPAGE@#@EXECUTABLE@ -@BCFTOOLS_WIKI@ +@BCFTOOLS_HOWTOS@ ]]> </help> <expand macro="citations" />