Mercurial > repos > iuc > bcftools_query
comparison bcftools_query.xml @ 16:3ce32adc55b2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
| author | iuc |
|---|---|
| date | Tue, 20 Sep 2022 13:12:13 +0000 |
| parents | 94c5f302f0ea |
| children |
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| 15:f64e7ca2efd2 | 16:3ce32adc55b2 |
|---|---|
| 1 <?xml version='1.0' encoding='utf-8'?> | 1 <?xml version='1.0' encoding='utf-8'?> |
| 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> | 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 3 <description>Extracts fields from VCF/BCF file and prints them in user-defined format</description> | 3 <description>Extracts fields from VCF/BCF file and prints them in user-defined format</description> |
| 4 <macros> | 4 <macros> |
| 5 <token name="@EXECUTABLE@">query</token> | 5 <token name="@EXECUTABLE@">query</token> |
| 6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
| 7 </macros> | 7 </macros> |
| 80 <param name="input_files" ftype="vcf" value="query.vcf" /> | 80 <param name="input_files" ftype="vcf" value="query.vcf" /> |
| 81 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> | 81 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> |
| 82 <param name="tsv" value="True" /> | 82 <param name="tsv" value="True" /> |
| 83 <output name="output_file" file="query.out" /> | 83 <output name="output_file" file="query.out" /> |
| 84 </test> | 84 </test> |
| 85 <!-- Test region overlap option--> | |
| 86 <test> | |
| 87 <param name="input_files" ftype="vcf" value="query.vcf" /> | |
| 88 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> | |
| 89 <param name="tsv" value="True" /> | |
| 90 <section name="sec_restrict"> | |
| 91 <param name="regions_overlap" value="1"/> | |
| 92 </section> | |
| 93 <output name="output_file" file="query.out" /> | |
| 94 <assert_command> | |
| 95 <has_text text="--regions-overlap" /> | |
| 96 </assert_command> | |
| 97 </test> | |
| 85 </tests> | 98 </tests> |
| 86 <help><![CDATA[ | 99 <help><![CDATA[ |
| 87 ===================================== | 100 ===================================== |
| 88 bcftools @EXECUTABLE@ | 101 bcftools @EXECUTABLE@ |
| 89 ===================================== | 102 ===================================== |