Mercurial > repos > iuc > delly_filter
view filter.xml @ 4:74f9f312c713 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
| author | iuc |
|---|---|
| date | Mon, 27 Jun 2022 18:16:33 +0000 |
| parents | d2590fe6793f |
| children |
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<?xml version="1.0"?> <tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> <description>somatic or germline structural variants</description> <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ ## initialize #if $input.is_of_type('vcf') bcftools view -Ob '$input' > 'input.bcf.gz' && bcftools index 'input.bcf.gz' && #else ln -s '${input}' 'input.bcf.gz' && ln -s '${input.metadata.bcf_index}' 'input.bcf.gz.csi' && #end if ## run delly filter ## generic options --filter $sv.mode_cond.mode_sel --outfile 'result.bcf' --altaf $generic.altaf --minsize $generic.minsize --maxsize $generic.maxsize --ratiogeno $generic.ratiogeno $generic.pass ## somatic options #if $sv.mode_cond.mode_sel == 'somatic' --samples '$sv.mode_cond.samples' --coverage $sv.mode_cond.coverage --controlcontamination $sv.mode_cond.controlcontamination ## germline options #else if $sv.mode_cond.mode_sel == 'germline' --gq $sv.mode_cond.gq --rddel $sv.mode_cond.rddel --rddup $sv.mode_cond.rddup #end if ## input 'input.bcf.gz' ## postprocessing @LOG@ @VCF@ ]]></command> <inputs> <expand macro="input" format="bcf,vcf" label="Select input file"/> <section name="generic" title="Generic options" expanded="true"> <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/> <expand macro="minsize" default="0" label="Set minimum SV size"/> <expand macro="maxsize" default="500000000" label="Set maximum SV size"/> <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/> <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> </section> <section name="sv" title="SV calling options" expanded="true"> <conditional name="mode_cond"> <param name="mode_sel" type="select" label="Select filter mode" help="(--filter)"> <option value="somatic" selected="true">Somatic</option> <option value="germline">Germline</option> </param> <when value="somatic"> <expand macro="samples"/> <expand macro="coverage" label="Set minimum coverage in tumor"/> <param argument="--controlcontamination" type="float" value="0.0" min="0.0" max="1.0" label="Set maximum fractional ALT support in control"/> </when> <when value="germline"> <param argument="--gq" type="integer" value="15" label="Set minimum median GQ for carriers and non-carriers"/> <param argument="--rddel" type="float" value="0.8" label="Set maximum read-depth ratio of carrier vs. non-carrier for a deletion"/> <param argument="--rddup" type="float" value="1.2" label="Set minimum read-depth ratio of carrier vs. non-carrier for a duplication"/> </when> </conditional> </section> <section name="oo" title="Output options" expanded="true"> <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> <option value="bcf" selected="true">BCF</option> <option value="log">Log</option> <option value="vcf">VCF</option> </param> </section> </inputs> <outputs> <expand macro="bcf"/> <expand macro="log"/> <expand macro="vcf"/> </outputs> <tests> <!-- #1 default, somatic, bcf --> <test expect_num_outputs="2"> <param name="input" value="call_1.bcf.gz"/> <section name="sv"> <conditional name="mode_cond"> <param name="mode_sel" value="somatic"/> <param name="samples" value="samples.tsv"/> </conditional> </section> <section name="oo"> <param name="out" value="vcf,bcf"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="2281" delta="10"/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> <has_n_lines n="140"/> <has_line line="##fileformat=VCFv4.2"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> </assert_contents> </output> </test> <!-- #2 somatic, bcf --> <test expect_num_outputs="3"> <param name="input" value="call_1.bcf.gz"/> <section name="generic"> <param name="altaf" value="0.3"/> <param name="minsize" value="1"/> <param name="maxsize" value="500000001"/> <param name="ratiogeno" value="0.76"/> <param name="pass" value="true"/> </section> <section name="sv"> <conditional name="mode_cond"> <param name="mode_sel" value="somatic"/> <param name="samples" value="samples.tsv"/> <param name="coverage" value="11"/> <param name="controlcontamination" value="0.1"/> </conditional> </section> <section name="oo"> <param name="out" value="vcf,bcf,log"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="2281" delta="10"/> </assert_contents> </output> <output name="out_log"> <assert_contents> <has_text_matching expression=".+Done\."/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> <has_n_lines n="140"/> <has_line line="##fileformat=VCFv4.2"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> </assert_contents> </output> </test> <!-- #3 default, germline, bcf --> <test expect_num_outputs="2"> <param name="input" value="call_1.bcf.gz"/> <section name="sv"> <conditional name="mode_cond"> <param name="mode_sel" value="germline"/> </conditional> </section> <section name="oo"> <param name="out" value="vcf,bcf"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="2264" delta="10"/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> <has_n_lines n="139"/> <has_line line="##fileformat=VCFv4.2"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> </assert_contents> </output> </test> <!-- #4 germline, bcf --> <test expect_num_outputs="3"> <param name="input" value="call_1.bcf.gz"/> <section name="generic"> <param name="altaf" value="0.1"/> <param name="minsize" value="1"/> <param name="maxsize" value="500000001"/> <param name="ratiogeno" value="0.76"/> <param name="pass" value="true"/> </section> <section name="sv"> <conditional name="mode_cond"> <param name="mode_sel" value="germline"/> <param name="gq" value="14"/> <param name="rddel" value="0.7"/> <param name="rddup" value="1.3"/> </conditional> </section> <section name="oo"> <param name="out" value="vcf,bcf,log"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="2264" delta="10"/> </assert_contents> </output> <output name="out_log"> <assert_contents> <has_text_matching expression=".+Done\."/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> <has_n_lines n="139"/> <has_line line="##fileformat=VCFv4.2"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> </assert_contents> </output> </test> <!-- #5 default, somatic, vcf --> <test expect_num_outputs="2"> <param name="input" value="call_1.vcf.gz"/> <section name="sv"> <conditional name="mode_cond"> <param name="mode_sel" value="somatic"/> <param name="samples" value="samples.tsv"/> </conditional> </section> <section name="oo"> <param name="out" value="vcf,bcf"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="2451" delta="10"/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> <has_n_lines n="143"/> <has_line line="##fileformat=VCFv4.2"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** @WID@ **Input** *Somatic* filtering requires a called SV input with at least one tumor sample and a matched control sample. In addition, a tab-delimited sample description needs to be provided, in which the first column holds the sample ids (as found in the VCF/BCF input) and the second column specifies either tumor or control. *Germline* SV calling is done by sample for high-coverage genomes or in small batches for low-coverage genomes. **Output** The output is available in BCF and VCF format. Additionally a log file is provided. .. class:: infomark **References** @REFERENCES@ ]]></help> <expand macro="citations"/> </tool>