Mercurial > repos > iuc > delly_call
diff call.xml @ 0:36772204dee5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
| author | iuc |
|---|---|
| date | Mon, 28 Sep 2020 07:45:21 +0000 |
| parents | |
| children | 53d90d86fc83 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/call.xml Mon Sep 28 07:45:21 2020 +0000 @@ -0,0 +1,291 @@ +<?xml version="1.0"?> +<tool id="delly_call" name="Delly call" version="@TOOL_VERSION@+galaxy0" 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 +#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 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 +--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="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="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="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 a output file for SV-reads is provided. + +.. class:: infomark + +**References** + +@REFERENCES@ + ]]></help> + <expand macro="citations"/> +</tool> \ No newline at end of file