Mercurial > repos > iuc > delly_filter
diff filter.xml @ 0:a75e05f20a66 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
| author | iuc |
|---|---|
| date | Mon, 28 Sep 2020 07:44:40 +0000 |
| parents | |
| children | 9919057a466c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter.xml Mon Sep 28 07:44:40 2020 +0000 @@ -0,0 +1,272 @@ +<?xml version="1.0"?> +<tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy0" profile="18.01"> + <description>somatic or germline structural variants</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ +## initialize +#if $samples.is_of_type('vcf') + bcftools view -Ob '$samples' > 'sample.bcf.gz' && + bcftools index 'sample.bcf.gz' && +#else + ln -s '${samples}' 'sample.bcf.gz' && + ln -s '${samples.metadata.bcf_index}' 'sample.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 +#end if +## germline options +#if $sv.mode_cond.mode_sel == 'germline' + --gq $sv.mode_cond.gq + --rddel $sv.mode_cond.rddel + --rddup $sv.mode_cond.rddup +#end if +## samples +'sample.bcf.gz' ## input + +## postprocessing +#if 'log' in $oo.out + |& tee 'log.txt' +#end if +#if 'vcf' in $oo.out + && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.' +#end if + ]]></command> + <inputs> + <expand macro="samples" format="bcf,vcf" multiple="false" label="Select 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"/> + <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/> + <param argument="--maxsize" type="integer" value="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 argument="mode_sel" type="select" label="Select filter mode"> + <option value="somatic" selected="true">Somatic</option> + <option value="germline">Germline</option> + </param> + <when value="somatic"> + <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/> + <param argument="--coverage" type="integer" value="10" 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"> + <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> + <option value="bcf" selected="true">BCF</option> + <option value="vcf">VCF</option> + <option value="log">Log</option> + </param> + </section> + </inputs> + <outputs> + <expand macro="vcf"/> + <expand macro="bcf"/> + <expand macro="log"/> + </outputs> + <tests> + <!-- #1 default, somatic, bcf --> + <test expect_num_outputs="2"> + <param name="samples" 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="samples" 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_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> + <output name="out_log"> + <assert_contents> + <has_text_matching expression=".+Done\."/> + </assert_contents> + </output> + </test> + <!-- #3 default, germline, bcf --> + <test expect_num_outputs="2"> + <param name="samples" 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="samples" 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_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> + <output name="out_log"> + <assert_contents> + <has_text_matching expression=".+Done\."/> + </assert_contents> + </output> + </test> + <!-- #5 default, somatic, vcf --> + <test expect_num_outputs="2"> + <param name="samples" 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="2440" delta="10"/> + </assert_contents> + </output> + <output name="out_vcf"> + <assert_contents> + <has_n_lines n="142"/> + <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@ + +Delly *filter* contains workflows for germline and somatic SV calling. + +**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. + +.. class:: infomark + +**References** + +@REFERENCES@ + ]]></help> + <expand macro="citations"/> +</tool> \ No newline at end of file