Mercurial > repos > iuc > delly_lr
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
| author | iuc |
|---|---|
| date | Mon, 28 Sep 2020 07:45:41 +0000 |
| parents | |
| children | d5124d5c8131 |
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<?xml version="1.0"?> <tool id="delly_lr" name="Delly long-read (lr)" version="@TOOL_VERSION@+galaxy0" profile="18.01"> <description>optimized calling and genotyping of structural variants</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) ln -s '${current}' 'sample_${i}.bam' && ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' && #end for ## run delly lr ## generic options --svtype $generic.svtype --technology $generic.technology --genome '$generic.genome' #if $generic.exclude --exclude '$generic.exclude' #end if --outfile 'result.bcf' ## discovery options --mapqual $discovery.mapqual --minclip $discovery.minclip --minrefsep $discovery.minrefsep --maxreadsep $discovery.maxreadsep ## genotyping options #if $genotyping.vcffile --vcffile '$genotyping.vcffile' #end if --geno-qual $genotyping.genoqual #if 'dump' in $oo.out --dump 'dump.tsv.gz' #end if ## samples #for $i, $current in enumerate($samples) 'sample_${i}.bam' #end for ## 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 #if 'dump' in $oo.out && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.' #end if ]]></command> <inputs> <expand macro="samples"/> <section name="generic" title="Generic options" expanded="true"> <expand macro="genome"/> <expand macro="svtype"/> <expand macro="exclude"/> <param argument="--technology" type="select" label="Select sequencing technology"> <option value="ont" selected="true">Oxford Nanopore (ont)</option> <option value="pb">Pacbio (pb)</option> </param> </section> <section name="discovery" title="Discovery options" expanded="true"> <param argument="--mapqual" type="integer" value="1" label="Set minimum mapping quality"/> <expand macro="minclip"/> <expand macro="minrefsep"/> <expand macro="maxreadsep"/> </section> <section name="genotyping" title="Genotyping options" expanded="true"> <expand macro="vcffile"/> <expand macro="genoqual"/> </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="dump">SV-reads</option> <option value="log">Log</option> </param> </section> </inputs> <outputs> <expand macro="vcf"/> <expand macro="bcf"/> <expand macro="dump"/> <expand macro="log"/> </outputs> <tests> <!-- no test implemented for parameter vcffile --> <!-- #1 default, single --> <test expect_num_outputs="2"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> </section> <section name="oo"> <param name="out" value="vcf,bcf"/> </section> <output name="out_vcf"> <assert_contents> <has_size value="3661" delta="10"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> </assert_contents> </output> <output name="out_bcf"> <assert_contents> <has_size value="1184" delta="10"/> </assert_contents> </output> </test> <!-- #2 default, multi; test data to small, results are empty --> <test expect_num_outputs="3"> <param name="samples" value="normal.bam,tumor.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> </section> <section name="oo"> <param name="out" value="vcf,bcf,log"/> </section> <output name="out_vcf"> <assert_contents> <has_size value="3667" delta="10"/> </assert_contents> </output> <output name="out_bcf"> <assert_contents> <has_size value="1189" delta="10"/> </assert_contents> </output> <output name="out_log"> <assert_contents> <has_text_matching expression=".+Done.+"/> </assert_contents> </output> </test> <!-- #3 --> <test expect_num_outputs="4"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="exclude" value="exclude.tsv"/> </section> <section name="oo"> <param name="out" value="vcf,bcf,dump,log"/> </section> <output name="out_vcf"> <assert_contents> <has_size value="3661" delta="10"/> </assert_contents> </output> <output name="out_bcf"> <assert_contents> <has_size value="1186" delta="10"/> </assert_contents> </output> <output name="out_dump"> <assert_contents> <has_n_lines n="0"/> </assert_contents> </output> <output name="out_log"> <assert_contents> <has_text_matching expression=".+Done.+"/> </assert_contents> </output> </test> <!-- #4 --> <test expect_num_outputs="4"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="svtype" value="DEL"/> <param name="technology" value="pb"/> </section> <section name="discovery"> <param name="mapqual" value="2"/> <param name="qualtra" value="19"/> <param name="madcutoff" value="8"/> <param name="minclip" value="24"/> <param name="minrefsep" value="24"/> <param name="maxreadsep" value="39"/> </section> <section name="genotyping"> <param name="genoqual" value="4"/> </section> <section name="oo"> <param name="out" value="vcf,bcf,dump,log"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="1182" delta="10"/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> <has_size value="3661" delta="10"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> </assert_contents> </output> <output name="out_dump"> <assert_contents> <has_size value="0"/> </assert_contents> </output> <output name="out_log"> <assert_contents> <has_text_matching expression=".+"/> </assert_contents> </output> </test> <!-- #5 --> <test expect_num_outputs="1"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="svtype" value="INS"/> </section> <section name="oo"> <param name="out" value="vcf"/> </section> <output name="out_vcf"> <assert_contents> <has_size value="3661" delta="10"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> </assert_contents> </output> </test> <!-- #6 --> <test expect_num_outputs="1"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="svtype" value="DUP"/> </section> <section name="oo"> <param name="out" value="bcf"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="1182" delta="10"/> </assert_contents> </output> </test> <!-- #7 --> <test expect_num_outputs="1"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="svtype" value="INV"/> </section> <section name="oo"> <param name="out" value="dump"/> </section> <output name="out_dump"> <assert_contents> <has_size value="0"/> </assert_contents> </output> </test> <!-- #8 --> <test expect_num_outputs="1"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="svtype" value="BND"/> </section> <section name="oo"> <param name="out" value="log"/> </section> <output name="out_log"> <assert_contents> <has_text_matching expression=".+"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** @WID@ Delly *lr* uses the long-read SV discovery mode. **Input** Delly *lr* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied. **Output** The output is available in BCF and VCF format. Additionally a output file for SV-reads is provided. .. class:: infomark **References** @REFERENCES@ ]]></help> <expand macro="citations"/> </tool>