Mercurial > repos > iuc > delly_lr
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit beb2da7c9ef39a0b0ed0d508d7521468500a86a0
| author | iuc |
|---|---|
| date | Fri, 19 Aug 2022 07:47:31 +0000 |
| parents | 7bd397ff21a2 |
| children |
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<?xml version="1.0"?> <tool id="delly_lr" name="Delly long-read (lr)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> <description>optimized calling and genotyping of 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 @BAM@ @FASTA@ ## run delly lr ## generic options --svtype $generic.svtype --technology $generic.technology --genome genome.fa #if $generic.exclude --exclude '$generic.exclude' #end if --outfile 'result.bcf' ## discovery options --mapqual $discovery.mapqual --minclip $discovery.minclip --min-clique-size $discovery.mincliquesize --minrefsep $discovery.minrefsep --maxreadsep $discovery.maxreadsep ## consensus options --max-reads $consensus.maxreads --flank-size $consensus.flanksize --flank-quality $consensus.flankquality ## genotyping options --geno-qual $genotyping.genoqual #if 'dump' in $oo.out --dump 'dump.tsv.gz' #end if ## input #for $i, $current in enumerate($input) 'input_${i}.bam' #end for ## postprocessing @LOG@ @DUMP@ @VCF@ ]]></command> <inputs> <expand macro="input" format="bam" multiple="true" label="Select input file(s)"/> <section name="generic" title="Generic options" expanded="true"> <expand macro="svtype"/> <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> <expand macro="genome"/> <expand macro="exclude"/> </section> <section name="discovery" title="Discovery options" expanded="true"> <param argument="--mapqual" type="integer" value="10" label="Set minimum mapping quality"/> <expand macro="minclip"/> <expand macro="mincliquesize"/> <expand macro="minrefsep" default="30"/> <expand macro="maxreadsep" default="75"/> </section> <section name="consensus" title="Consensus options" expanded="true"> <param name="maxreads" type="integer" value="5" label="Set maximum reads for consensus computation" help="(--max-reads)"/> <param name="flanksize" type="integer" value="400" label="Set minimum flank size" help="(--flank-size)"/> <param name="flankquality" type="float" min="0.0" max="1.0" value="0.9" label="Set minimum flank quality" help="(--flank-quality)"/> </section> <section name="genotyping" title="Genotyping options" expanded="true"> <expand macro="genoqual"/> </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="dump">SV-reads</option> <option value="vcf">VCF</option> </param> </section> </inputs> <outputs> <expand macro="bcf"/> <expand macro="dump"/> <expand macro="log"/> <expand macro="vcf"/> </outputs> <tests> <!-- #1 default, single --> <test expect_num_outputs="2"> <param name="input" 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_bcf"> <assert_contents> <has_size value="1127" delta="10"/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> <has_n_lines n="46"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> </assert_contents> </output> </test> <!-- #2 default, multi; test data to small, results are empty --> <test expect_num_outputs="3"> <param name="input" 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_bcf"> <assert_contents> <has_size value="1131" 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="46"/> </assert_contents> </output> </test> <!-- #3 --> <test expect_num_outputs="4"> <param name="input" 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_bcf"> <assert_contents> <has_size value="1127" 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> <output name="out_vcf"> <assert_contents> <has_n_lines n="46"/> </assert_contents> </output> </test> <!-- #4 --> <test expect_num_outputs="4"> <param name="input" 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="mincliquesize" value="1"/> <param name="minrefsep" value="24"/> <param name="maxreadsep" value="39"/> </section> <section name="consensus"> <param name="maxreads" value="6"/> <param name="flanksize" value="399"/> <param name="flankquality" value="0.91"/> </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="1127" delta="10"/> </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> <output name="out_vcf"> <assert_contents> <has_n_lines n="46"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> </assert_contents> </output> </test> <!-- #5 --> <test expect_num_outputs="1"> <param name="input" 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_n_lines n="46"/> <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="input" 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="1127" delta="10"/> </assert_contents> </output> </test> <!-- #7 --> <test expect_num_outputs="1"> <param name="input" 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="input" 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@ **Input** Delly *long-read (lr)* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. **Output** The output is available in BCF and VCF format. Additionally an output file for SV-reads and a log file are provided. .. class:: infomark **References** @REFERENCES@ ]]></help> <expand macro="citations"/> </tool>