Mercurial > repos > iuc > delly_merge
view merge.xml @ 1:97c7441aed0d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
author | iuc |
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date | Thu, 29 Oct 2020 20:51:37 +0000 |
parents | 6331d804f983 |
children | 148389992630 |
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<?xml version="1.0"?> <tool id="delly_merge" name="Delly merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> <description>structural variants across/within VCF/BCF file(s)</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ ## initialize #for $i, $current in enumerate($samples) #if $current.is_of_type('vcf') bcftools view -Ob '$current' > 'sample_${i}.bcf.gz' && bcftools index 'sample_${i}.bcf.gz' && #else ln -s '${current}' 'sample_${i}.bcf.gz' && ln -s '${current.metadata.bcf_index}' 'sample_${i}.bcf.gz.csi' && #end if #end for ## run delly merge ## generic options --outfile 'result.bcf' --chunks $generic.chunks --vaf $generic.vaf --coverage $generic.coverage --minsize $generic.minsize --maxsize $generic.maxsize $generic.precise $generic.pass ## overlap options --bp-offset $overlap.bpoffset --rec-overlap $overlap.recoverlap ## samples #for $i, $current in enumerate($samples) 'sample_${i}.bcf.gz' #end for ## postprocessing @LOG@ @VCF@ ]]></command> <inputs> <expand macro="samples" format="bcf,vcf"/> <section name="generic" title="Generic options" expanded="true"> <param argument="--chunks" type="integer" value="500" label="Set maximum chunk size to merge groups of BCF files"/> <param argument="--vaf" type="float" value="0.15" min="0.0" max="1.0" label="Set minimum fractional ALT support"/> <param argument="--coverage" type="integer" value="10" label="Set minimum coverage"/> <expand macro="minsize"/> <expand macro="maxsize"/> <param argument="--precise" type="boolean" truevalue="--precise" falsevalue="" label="Filter sites for PRECISE?"/> <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> </section> <section name="overlap" title="Overlap options" expanded="true"> <param name="bpoffset" type="integer" value="1000" label="Set maximum breakpoint offset" help="(--bp-offset)"/> <param name="recoverlap" type="float" value="0.8" label="Set minimum reciprocal overlap" help="(--rec-overlap)"/> </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, bcf --> <test expect_num_outputs="2"> <param name="samples" value="call_1.bcf.gz,call_2.bcf.gz"/> <section name="oo"> <param name="out" value="vcf,bcf"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="1851" delta="10"/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> <has_n_lines n="128"/> <has_line line="##fileformat=VCFv4.2"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"/> </assert_contents> </output> </test> <!-- #2 bcf--> <test expect_num_outputs="3"> <param name="samples" value="call_1.bcf.gz,call_2.bcf.gz"/> <section name="generic"> <param name="chunks" value="500"/> <param name="vaf" value="0.16"/> <param name="coverage" value="10"/> <param name="minsize" value="0"/> <param name="maxsize" value="1000000"/> <param name="precise" value="true"/> <param name="pass" value="true"/> </section> <section name="overlap"> <param name="bp-offset" value="1000"/> <param name="rec-overlap" value="0.79"/> </section> <section name="oo"> <param name="out" value="vcf,bcf,log"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="1851" delta="10"/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> <has_n_lines n="128"/> <has_line line="##fileformat=VCFv4.2"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"/> <has_text_matching expression="chr5	75911568.+"/> </assert_contents> </output> <output name="out_log"> <assert_contents> <has_text_matching expression=".+Done\."/> </assert_contents> </output> </test> <!-- #3 default, vcf --> <test expect_num_outputs="2"> <param name="samples" value="call_1.vcf.gz,call_2.vcf.gz"/> <section name="oo"> <param name="out" value="vcf,bcf"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="1851" delta="10"/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> <has_n_lines n="128"/> <has_line line="##fileformat=VCFv4.2"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** @WID@ Delly *merge* merges SV sites into a unified site list. **Input** BCF or VCF files. **Output** A single BCF file. .. class:: infomark **References** @REFERENCES@ ]]></help> <expand macro="citations"/> </tool>