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view bcftools_convert_to_vcf.xml @ 16:ecc9192912b8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author | iuc |
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date | Tue, 20 Sep 2022 13:16:15 +0000 (2022-09-20) |
parents | 41873b29860a |
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<?xml version='1.0' encoding='utf-8'?> <tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Converts other formats to VCF/BCFk</description> <macros> <token name="@EXECUTABLE@">convert</token> <import>macros.xml</import> </macros> <expand macro="bio_tools" /> <expand macro="requirements"> <expand macro="samtools_requirement"/> </expand> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ @PREPARE_ENV@ #set $input_vcf = None #if $convert.convert_from == 'gvcf': #set $input_vcf = 'input.vcf.gz' #if $convert.input_file.is_of_type('vcf') bgzip -c '$convert.input_file' > $input_vcf && bcftools index $input_vcf && #elif $convert.input_file.is_of_type('vcf_bgzip') ln -s '$convert.input_file' $input_vcf #elif $convert.input_file.is_of_type('bcf') #set $input_vcf = 'input.bcf' ln -s '$convert.input_file' $input_vcf && bcftools index $input_vcf && #elif $convert.input_file.is_of_type('bcf_bgzip') ln -s '$convert.input_file' $input_vcf && #end if #end if #if $convert.convert_from == 'gvcf' or $convert.convert_from == 'tsv': #set $section = $convert.reference_source @PREPARE_FASTA_REF@ #end if bcftools @EXECUTABLE@ @OUTPUT_TYPE@ #if $convert.convert_from == 'gen_sample': --gensample2vcf '$convert.input_file,$convert.input_sample' #elif $convert.convert_from == 'hap_sample': --hapsample2vcf '$convert.input_file,$convert.input_sample' #elif $convert.convert_from == 'hap_legend_sample': --haplegendsample2vcf '$convert.input_file,$convert.input_legend,$convert.input_sample' #elif $convert.convert_from == 'gvcf': @FASTA_REF@ --gvcf2vcf $input_vcf #elif $convert.convert_from == 'tsv': @FASTA_REF@ #set $section = $convert @SAMPLES@ @COLUMNS@ --tsv2vcf '$convert.input_file' #end if > '$output_file' ]]> </command> <inputs> <conditional name="convert"> <param name="convert_from" type="select" label="convert from"> <option value="tsv">tsv - TAB-Separated-Value (e.g. 23andMe)</option> <option value="gvcf">gVCF - GATK Variant Call Format</option> <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option> <option value="hap_sample">haps sample - IMPUTE2 or SHAPEIT</option> <option value="hap_legend_sample">haps legend sample - IMPUTE2 or SHAPEIT</option> </param> <when value="tsv"> <param name="input_file" type="data" format="tabular" label="Tabular Variant Data" help="Reference sequence and samples are required"/> <expand macro="macro_fasta_ref" /> <expand macro="macro_samples"/> <expand macro="macro_columns"/> </when> <when value="gvcf"> <param name="input_file" type="data" format="vcf" label="Genomic VCF (GATK HaplotypeCaller)" /> <expand macro="macro_fasta_ref" /> </when> <when value="gen_sample"> <param name="input_file" type="data" format="tabular" label="The .gen file" /> <param name="input_sample" type="data" format="tabular" label="The .samples file" /> </when> <when value="hap_sample"> <param name="input_file" type="data" format="tabular" label="The .hap file" /> <param name="input_sample" type="data" format="tabular" label="The .samples file" /> </when> <when value="hap_legend_sample"> <param name="input_file" type="data" format="tabular" label="The .hap file" /> <param name="input_legend" type="data" format="tabular" label="The .legend file" /> <param name="input_sample" type="data" format="tabular" label="The .samples file" /> </when> </conditional> <expand macro="macro_select_output_type" /> </inputs> <outputs> <expand macro="macro_vcf_output"/> </outputs> <tests> <test> <conditional name="convert"> <param name="convert_from" value="gen_sample" /> <param name="input_file" ftype="tabular" value="convert.gs.gt.gen" /> <param name="input_sample" ftype="tabular" value="convert.gs.gt.samples" /> </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" /> <has_text_matching expression="X\t2698560\t.\tG\tA\t.\t.\t.\tGT:GP" /> </assert_contents> </output> </test> <test> <conditional name="convert"> <param name="convert_from" value="hap_sample" /> <param name="input_file" ftype="tabular" value="convert.hs.gt.hap" /> <param name="input_sample" ftype="tabular" value="convert.hs.gt.samples" /> </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" /> <has_text_matching expression="X\t2698769\t.\tAAG\tA\t.\t.\t.\tGT\t1|0\t1|1\t0|1\t1|0\t1|0\t0|0\t0|0\t0|0\t0|0\t0|0" /> </assert_contents> </output> </test> <test> <conditional name="convert"> <param name="convert_from" value="hap_legend_sample" /> <param name="input_file" ftype="tabular" value="convert.hls.gt.hap" /> <param name="input_legend" ftype="tabular" value="convert.hls.gt.legend" /> <param name="input_sample" ftype="tabular" value="convert.hls.gt.samples" /> </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" /> <has_text_matching expression="X\t2698769\t.\tAAG\tA\t.\t.\t.\tGT\t1|0\t1|1\t0|1\t1|0\t1|0\t0|0\t0|0\t0|0\t0|0\t0|0" /> </assert_contents> </output> </test> <test> <conditional name="convert"> <param name="convert_from" value="gvcf" /> <param name="input_file" ftype="vcf" value="convert.gvcf.vcf" /> <expand macro="test_using_reference" ref="gvcf.fa" /> </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" /> <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" /> </assert_contents> </output> </test> <test> <conditional name="convert"> <param name="convert_from" value="gvcf" /> <param name="input_file" ftype="vcf" dbkey="?" value="convert.gvcf.vcf" /> <expand macro="test_using_reference" select_from="cached" ref="gvcf" /> </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" /> <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" /> </assert_contents> </output> </test> <test> <conditional name="convert"> <param name="convert_from" value="tsv" /> <param name="input_file" ftype="tabular" value="convert.23andme" /> <expand macro="test_using_reference" ref="23andme.fa" /> <param name="samples" value="SAMPLE1" /> <param name="columns" value="ID,CHROM,POS,AA" /> </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" /> <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" /> </assert_contents> </output> </test> <test> <conditional name="convert"> <param name="convert_from" value="tsv" /> <param name="input_file" ftype="tabular" dbkey="?" value="convert.23andme" /> <expand macro="test_using_reference" select_from="cached" ref="23andme" /> <param name="samples" value="SAMPLE1" /> <param name="columns" value="ID,CHROM,POS,AA" /> </conditional> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" /> <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ ===================================== bcftools @EXECUTABLE@ plugin ===================================== Converts other variant formats to vcf. See man page for file formats details. @BCFTOOLS_MANPAGE@#@EXECUTABLE@ @BCFTOOLS_WIKI@ ]]> </help> <expand macro="citations" /> </tool>