Mercurial > repos > iuc > bcftools_stats
diff bcftools_stats.xml @ 16:4d3ce9dc1525 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author | iuc |
---|---|
date | Tue, 20 Sep 2022 12:54:05 +0000 |
parents | 80844da35ed5 |
children | a2f8dc22d7c0 |
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--- a/bcftools_stats.xml Sat Jul 23 13:50:21 2022 +0000 +++ b/bcftools_stats.xml Tue Sep 20 12:54:05 2022 +0000 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1" profile="18.01"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description> <macros> <token name="@EXECUTABLE@">stats</token> @@ -198,6 +198,49 @@ </output> <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" /> </test> + <!-- Test region overlap option--> + <test> + <param name="input_file" ftype="vcf" value="stats.b.vcf" /> + <param name="inputB_file" ftype="vcf" value="stats.a.vcf" /> + <section name="sec_restrict"> + <param name="regions_overlap" value="1"/> + </section> + <output name="output_file"> + <assert_contents> + <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> + <has_text_matching expression="SN\t1\tnumber of samples:\t3"/> + </assert_contents> + </output> + <assert_command> + <has_text text="--regions-overlap" /> + </assert_command> + </test> + <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605 + <test> + <param name="input_file" value="mpileup.vcf.gz" /> + <output name="output_file"> + <assert_contents> + <has_text_matching expression="bcftools stats input0.vcf.gz"/> + <has_text_matching expression="SN\t0\tnumber of samples:\t3"/> + <has_text_matching expression="SN\t0\tnumber of records:\t4103"/> + </assert_contents> + </output> + </test> + --> + <!-- Test modification in samples option --> + <test> + <param name="input_file" ftype="vcf" value="mpileup.vcf" /> + <section name="sec_restrict"> + <param name="samples" value="-" /> + </section> + <output name="output_file"> + <assert_contents> + <has_text_matching expression="bcftools stats --samples - "/> + <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.8"/> + <has_text_matching expression="PSI\t0\tHG00102\t0"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ =====================================