Mercurial > repos > iuc > delly_lr
view macros.xml @ 4:7bd397ff21a2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
author | iuc |
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date | Mon, 27 Jun 2022 18:17:41 +0000 |
parents | d30785dbe6b7 |
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<?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">0.9.1</token> <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">delly</requirement> <requirement type="package" version="1.12">bcftools</requirement> </requirements> </xml> <xml name="version_command"> <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command> </xml> <xml name="citations"> <citations> <citation type="doi">10.1093/bioinformatics/bts378</citation> </citations> </xml> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">delly2</xref> </xrefs> </xml> <!-- command --> <token name="@SINGLE_BAM@"><![CDATA[ ln -s '$input' 'input.bam' && ln -s '$input.metadata.bam_index' 'input.bam.bai' && ]]></token> <token name="@BAM@"><![CDATA[ #for $i, $current in enumerate($input) ln -s '${current}' 'input_${i}.bam' && ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' && #end for ]]></token> <!-- fasta needs to be linked, because .fai file is created --> <token name="@FASTA@"><![CDATA[ ln -s '$generic.genome' genome.fa && ]]></token> <token name="@DUMP@"><![CDATA[ #if 'dump' in $oo.out && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.' #end if ]]></token> <token name="@LOG@"><![CDATA[ #if 'log' in $oo.out |& tee '$out_log' #end if ]]></token> <token name="@VCF@"><![CDATA[ #if 'vcf' in $oo.out && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.' #end if ]]></token> <!-- input --> <xml name="cnoffset" token_default=""> <param name="cnoffset" type="float" min="0.0" max="1.0" value="@DEFAULT@" label="Set minimum CN offset" help="(--cn-offset)"/> </xml> <xml name="coverage" token_label=""> <param argument="--coverage" type="integer" value="10" label="@LABEL@"/> </xml> <xml name="exclude"> <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/> </xml> <xml name="genome"> <param argument="--genome" type="data" format="fasta" label="Select genome file"/> </xml> <xml name="genoqual"> <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/> </xml> <xml name="input" token_format="" token_multiple="false" token_label=""> <param name="input" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/> </xml> <xml name="maxreadsep" token_default=""> <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/> </xml> <xml name="maxsize" token_default="" token_label=""> <param argument="--maxsize" type="integer" value="@DEFAULT@" label="@LABEL@"/> </xml> <xml name="minclip"> <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/> </xml> <xml name="mincliquesize"> <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/> </xml> <xml name="minrefsep" token_default=""> <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/> </xml> <xml name="minsize" token_default="" token_label=""> <param argument="--minsize" type="integer" value="@DEFAULT@" label="@LABEL@"/> </xml> <xml name="pass"> <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> </xml> <xml name="ploidy"> <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/> </xml> <xml name="samples"> <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/> </xml> <xml name="svtype"> <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect"> <option value="ALL" selected="true">All types (ALL)</option> <option value="DEL">Deletion (DEL)</option> <option value="DUP">Duplication (DUP)</option> <option value="INS">Insertion (INS)</option> <option value="INV">Inversion (INV)</option> <option value="BND">Translocation (BND)</option> </param> </xml> <xml name="vcffile"> <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/> </xml> <!-- output --> <xml name="bcf"> <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)"> <filter>'bcf' in oo['out']</filter> </data> </xml> <xml name="vcf"> <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)"> <filter>'vcf' in oo['out']</filter> </data> </xml> <xml name="dump"> <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads"> <filter>'dump' in oo['out']</filter> </data> </xml> <xml name="log"> <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> <filter>'log' in oo['out']</filter> </data> </xml> <!-- help --> <token name="@WID@"><![CDATA[ Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. Short-read SV calling - *call* to discover and genotype structural variants - *merge* structural variants across VCF/BCF files and within a single VCF/BCF file - *filter* somatic or germline structural variants Long-read SV calling - *lr* for long-read SV discovery Copy-number variant calling - *cnv* to discover and genotype copy-number variants - *classify* somatic or germline copy-number variants ]]></token> <token name="@REFERENCES@"><![CDATA[ More information are available on `GitHub <https://github.com/dellytools/delly>`_. ]]></token> </macros>