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view bcftools_norm.xml @ 3:a01eacacfd88 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
author | iuc |
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date | Tue, 31 Jan 2017 12:43:24 -0500 |
parents | d110fb275304 |
children | 660f8eec689d |
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<?xml version='1.0' encoding='utf-8'?> <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1"> <description>Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows</description> <macros> <token name="@EXECUTABLE@">norm</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ @PREPARE_ENV@ @PREPARE_INPUT_FILE@ #set $section = $sec_ref @PREPARE_FASTA_REF@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ bcftools @EXECUTABLE@ #set $section = $sec_ref @FASTA_REF@ ${section.do_not_normalize} #if $section.check_ref: --check-ref "${section.check_ref}" #end if ## Default section #set $section = $sec_default #if $section.rm_dup: --rm-dup "${section.rm_dup}" #end if #if $section.multiallelics: #set $mtype = '' #if $section.multiallelic_types: #set $mtype = $section.multiallelic_types #end if --multiallelics "${section.multiallelics}${mtype}" #end if ${section.strict_filter} #if $section.site_win: --site-win "${section.site_win}" #end if #set $section = $sec_restrict @REGIONS@ @TARGETS@ @OUTPUT_TYPE@ @THREADS@ ## Primary Input/Outputs @INPUT_FILE@ > "$output_file" ]]> </command> <inputs> <expand macro="macro_input" /> <section name="sec_restrict" expanded="false" title="Restrict to"> <expand macro="macro_regions" /> <expand macro="macro_targets" /> </section> <section name="sec_ref" expanded="false" title="Reference Options"> <expand macro="macro_fasta_ref" /> <param name="check_ref" type="select" label="Check REF" optional="true" help="What to do when incorrect or missing REF allele is encountered"> <option value="e">check REF alleles and exit (e)</option> <option value="w">warn (w)</option> <option value="x">exclude (x)</option> <option value="s">set bad sites (s)</option> <option value="wx">warn and exclude (wx)</option> <option value="ws">warn and set bad sites (ws)</option> </param> <param name="do_not_normalize" type="boolean" truevalue="--do-not-normalize" falsevalue="" label="Skip Normalization, just set REF allele" help="Do not normalize indels, just fix or set the REF allele from the reference (-N, --do-not-normalize with -m or -c s)" /> </section> <section name="sec_default" expanded="false" title="Default Options"> <param name="rm_dup" type="select" label="Rm Dup" optional="true" help="Remove duplicate snps|indels|both|any"> <option value="snps">snps</option> <option value="indels">indels</option> <option value="both">both</option> <option value="any">any</option> </param> <param name="multiallelics" type="select" label="~multiallelics" optional="true"> <option value="-">split multiallelic sites into biallelic records (-)</option> <option value="+">join biallelic sites into multiallelic records (+)</option> </param> <param name="multiallelic_types" type="select" label="variant types which should be split or merged" optional="true"> <option value="snps">snps - only SNP records should be split or merged</option> <option value="indels">indels - only indel records should be split or merged</option> <option value="both">both - records should be split or merged</option> <option value="any">any - SNPs and indels should be merged into a single record</option> </param> <param name="strict_filter" type="boolean" truevalue="--strict-filter" falsevalue="" label="Strict Filter" help="When merging (-m+), merged site is PASS only if all sites being merged PASS" /> <param name="site_win" type="integer" label="Site Window" value="1000" optional="True" help="(-w, --site-win) Buffer for sorting lines which changed position during realignment" /> </section> <expand macro="macro_select_output_type" /> </inputs> <outputs> <expand macro="macro_vcf_output"/> </outputs> <tests> <test> <param name="input_file" ftype="vcf" value="norm.vcf" /> <param name="fasta_ref" ftype="fasta" value="norm.fa" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text text="T,TAACCCTA" /> <not_has_text text="TAA,TAACCCTAAA" /> </assert_contents> </output> </test> <test> <param name="input_file" ftype="vcf" value="norm.split.vcf" /> <param name="multiallelics" value="-" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <not_has_text text="TAA,TAACCCTAAA" /> <has_text_matching expression="1\t105\t.\tTAAACCCTAAA\tTAA\t"/> <has_text_matching expression="1\t105\t.\tTAAACCCTAAA\tTAACCCTAAA\t"/> </assert_contents> </output> </test> <test> <param name="input_file" ftype="vcf" value="norm.split.vcf" /> <param name="fasta_ref" ftype="fasta" value="norm.fa" /> <param name="multiallelics" value="-" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <not_has_text text="TAA,TAACCCTAAA" /> <has_text_matching expression="1\t105\t.\tTAAACCCTA\tT\t"/> <has_text_matching expression="1\t105\t.\tTA\tT\t"/> </assert_contents> </output> </test> <test> <param name="input_file" ftype="vcf" value="norm.merge.vcf" /> <param name="multiallelics" value="+" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text text="TAA,TAACCCTAAA" /> <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tFAIL"/> </assert_contents> </output> </test> <test> <param name="input_file" ftype="vcf" value="norm.merge.vcf" /> <param name="multiallelics" value="+" /> <param name="strict_filter" value="true" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text text="TAA,TAACCCTAAA" /> <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tPASS"/> </assert_contents> </output> </test> <test> <param name="input_file" ftype="vcf" value="norm.setref.vcf" /> <param name="fasta_ref" ftype="fasta" value="norm.fa" /> <param name="do_not_normalize" value="true" /> <param name="check_ref" value="s" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text_matching expression="2\t101\t.\tA\tc\t999\tPASS"/> <has_text_matching expression="2\t105\t.\tT\t<DEL>\t999\tPASS"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ ===================================== bcftools @EXECUTABLE@ ===================================== Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows. @REGIONS_HELP@ @TARGETS_HELP@ @BCFTOOLS_MANPAGE@#@EXECUTABLE@ @BCFTOOLS_WIKI@ ]]> </help> <expand macro="citations" /> </tool>