Mercurial > repos > iuc > delly_call
view call.xml @ 1:53d90d86fc83 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
| author | iuc |
|---|---|
| date | Thu, 29 Oct 2020 20:50:39 +0000 |
| parents | 36772204dee5 |
| children | 9946bd542898 |
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<?xml version="1.0"?> <tool id="delly_call" name="Delly call" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> <description>and genotype structural variants</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ ## initialize @BAM@ ## run delly call ## generic options --svtype $generic.svtype --genome '$generic.genome' #if $generic.exclude --exclude '$generic.exclude' #end if --outfile 'result.bcf' ## discovery options --map-qual $discovery.mapqual --qual-tra $discovery.qualtra --mad-cutoff $discovery.madcutoff --minclip $discovery.minclip --min-clique-size $discovery.mincliquesize --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 @LOG@ @VCF@ @DUMP@ ]]></command> <inputs> <expand macro="samples"/> <section name="generic" title="Generic options" expanded="true"> <expand macro="svtype"/> <expand macro="genome"/> <expand macro="exclude"/> </section> <section name="discovery" title="Discovery options" expanded="true"> <param name="mapqual" type="integer" value="1" label="Set minimum paired-end (PE) mapping quality" help="(--map-qual)"/> <param name="qualtra" type="integer" value="20" label="Set minimum PE quality for translocation" help="(--qual-tra)"/> <param name="madcutoff" type="integer" value="9" label="Set insert size cutoff" help="median+s*MAD, deletions only (--mad-cutoff)"/> <expand macro="minclip"/> <expand macro="mincliquesize"/> <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 (--dump)</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="0"/> </assert_contents> </output> <output name="out_bcf"> <assert_contents> <has_size value="0"/> </assert_contents> </output> <output name="out_log"> <assert_contents> <has_text_matching expression="Sample has not enough data to estimate library parameters.+"/> </assert_contents> </output> </test> <!-- #3; results are empty due to exclude file --> <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="0"/> </assert_contents> </output> <output name="out_bcf"> <assert_contents> <has_size value="0"/> </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="Sample has not enough data to estimate library parameters.+"/> </assert_contents> </output> </test> <!-- #4 --> <test expect_num_outputs="1"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="svtype" value="ALL"/> <param name="genome" value="genome.fasta"/> </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="genotyping"> <param name="genoqual" value="4"/> </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> <!-- #5 --> <test expect_num_outputs="1"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="svtype" value="DEL"/> <param name="genome" value="genome.fasta"/> </section> <section name="oo"> <param name="out" value="bcf"/> </section> <output name="out_bcf"> <assert_contents> <has_size value="1183" delta="10"/> </assert_contents> </output> </test> <!-- #6 --> <test expect_num_outputs="1"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="svtype" value="INS"/> <param name="genome" value="genome.fasta"/> </section> <section name="oo"> <param name="out" value="dump"/> </section> <output name="out_dump"> <assert_contents> <has_size value="0"/> </assert_contents> </output> </test> <!-- #7 --> <test expect_num_outputs="1"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="svtype" value="INV"/> <param name="genome" value="genome.fasta"/> </section> <section name="oo"> <param name="out" value="log"/> </section> <output name="out_log"> <assert_contents> <has_text_matching expression=".+Done.+"/> </assert_contents> </output> </test> <!-- #8 --> <test expect_num_outputs="2"> <param name="samples" value="normal.bam"/> <section name="generic"> <param name="svtype" value="BND"/> <param name="genome" value="genome.fasta"/> </section> <section name="oo"> <param name="out" value="vcf,log"/> </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_log"> <assert_contents> <has_text_matching expression=".+Done.+"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** @WID@ **Input** Delly *call* 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 an output file for SV-reads is provided. .. class:: infomark **References** @REFERENCES@ ]]></help> <expand macro="citations"/> </tool>