Mercurial > repos > jjohnson > bcftools_convert_from_vcf
diff bcftools_convert_from_vcf.xml @ 0:d396503fdbdb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
| author | jjohnson |
|---|---|
| date | Sat, 25 Jun 2016 20:47:20 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_convert_from_vcf.xml Sat Jun 25 20:47:20 2016 -0400 @@ -0,0 +1,185 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool name="bcftools @EXECUTABLE@ from vcf" id="bcftools_@EXECUTABLE@_from_vcf" version="@VERSION@.0"> + <description>Converts VCF/BCF to IMPUTE2/SHAPEIT formats</description> + <macros> + <token name="@EXECUTABLE@">convert</token> + <import>macros.xml</import> + <xml name="macro_vcf_ids"> + <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" checked="false" + label="Output VCF IDs instead of CHROM:POS_REF_ALT" help="(\-\-vcf_ids)"/> + </xml> + <xml name="macro_haploid2diploid"> + <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" + label="convert haploid genotypes to diploid homozygotes" help="(\-\-haploid2diploid)"/> + </xml> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="aggressive"><![CDATA[ +@PREPARE_ENV@ +@PREPARE_INPUT_FILE@ +#set $section = $sec_restrict +@PREPARE_TARGETS_FILE@ + +bcftools @EXECUTABLE@ + +#if $convert.convert_to == 'gen_sample': +--tag $convert.tag $convert.chrom $convert.vcf_ids +--gensample "$output_gen,$output_samples" +#elif $convert.convert_to == 'hap_sample': +$convert.vcf_ids $convert.haploid2diploid +--hapsample "$output_hap,$output_samples" +#elif $convert.convert_to == 'hap_legend_sample': +$convert.vcf_ids $convert.haploid2diploid +--haplegendsample "$output_hap,$output_legend,$output_samples" +#end if + +## VCF input section +#set $section = $sec_restrict +@INCLUDE@ +@EXCLUDE@ +@REGIONS@ +@TARGETS@ +@SAMPLES@ + +## Primary Input/Outputs +"$input_file" . +]]> + </command> + <inputs> + <expand macro="macro_input" /> + <section name="sec_restrict" expanded="false" title="Restrict to"> + <expand macro="macro_regions" /> + <expand macro="macro_targets" /> + <expand macro="macro_samples" /> + <expand macro="macro_include" /> + <expand macro="macro_exclude" /> + </section> + <conditional name="convert"> + <param name="convert_to" type="select" label="convert to"> + <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option> + <option value="hap_sample">hap sample - IMPUTE2 or SHAPEIT</option> + <option value="hap_legend_sample">hap legend sample - IMPUTE2 or SHAPEIT</option> + </param> + <when value="gen_sample"> + <param name="tag" type="select" label="tag to take values for .gen file: GT,PL,GL,GP"> + <option value="GT">GT</option> + <option value="PL">PL</option> + <option value="GP">GP</option> + <!-- + <option value="GL">GL</option> + --> + </param> + <param name="chrom" type="boolean" truevalue="--chrom" falsevalue="" checked="false" + label="Output chromosome in first column instead of CHROM:POS_REF_ALT" help="(\-\-chrom)"/> + <expand macro="macro_vcf_ids"/> + </when> + <when value="hap_sample"> + <expand macro="macro_haploid2diploid"/> + <expand macro="macro_vcf_ids"/> + </when> + <when value="hap_legend_sample"> + <expand macro="macro_haploid2diploid"/> + <expand macro="macro_vcf_ids"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_gen" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.gen"> + <filter>convert['convert_to'] == 'gen_sample'</filter> + </data> + <data name="output_hap" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.haps"> + <filter>convert['convert_to'] in ('hap_sample','hap_legend_sample')</filter> + </data> + <data name="output_legend" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.legend"> + <filter>convert['convert_to'] == 'hap_legend_sample'</filter> + </data> + <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/> + </outputs> + <tests> + <test> + <param name="input_file" ftype="vcf" value="convert.vcf" /> + <param name="convert_to" value="gen_sample" /> + <output name="output_gen"> + <assert_contents> + <has_text text="X:2698560_G_A X:2698560_G_A 2698560 G A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0"/> + </assert_contents> + </output> + <output name="output_samples"> + <assert_contents> + <has_text text="NA00001 NA00001 0"/> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="convert.vcf" /> + <param name="convert_to" value="gen_sample" /> + <param name="tag" value="GP" /> + <param name="chrom" value="True" /> + <output name="output_gen"> + <assert_contents> + <has_text text="X X:2698560_G_A 2698560 G A 1.00"/> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="check.vcf" /> + <param name="convert_to" value="gen_sample" /> + <param name="tag" value="GT" /> + <param name="chrom" value="True" /> + <param name="vcf_ids" value="True" /> + <output name="output_gen"> + <assert_contents> + <has_text text="1 id3D 3062915 GTTT G 0 1 0 0 1 0"/> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="convert.vcf" /> + <param name="convert_to" value="hap_sample" /> + <output name="output_hap"> + <assert_contents> + <has_text text="X X:2698769_AAG_A 2698769 AAG A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="convert.vcf" /> + <param name="convert_to" value="hap_legend_sample" /> + <output name="output_hap"> + <assert_contents> + <has_text text="1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/> + </assert_contents> + </output> + <output name="output_legend"> + <assert_contents> + <has_text text="X:2698769_AAG_A 2698769 AAG A"/> + </assert_contents> + </output> + <output name="output_samples"> + <assert_contents> + <has_text text="sample population group sex"/> + <has_text text="NA00001 NA00001 NA00001 2"/> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +===================================== + bcftools @EXECUTABLE@ from vcf +===================================== + +Converts VCF/BCF to other formats. See man page for file formats details. + +@REGIONS_HELP@ +@TARGETS_HELP@ +@EXPRESSIONS_HELP@ + +@BCFTOOLS_MANPAGE@#@EXECUTABLE@ + +@BCFTOOLS_WIKI@ +]]> + </help> + <expand macro="citations" /> +</tool>