Mercurial > repos > iuc > delly_lr
diff lr.xml @ 2:ceda4714f3a1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
| author | iuc |
|---|---|
| date | Fri, 22 Jan 2021 14:32:45 +0000 |
| parents | d5124d5c8131 |
| children | d30785dbe6b7 |
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--- a/lr.xml Thu Oct 29 20:51:54 2020 +0000 +++ b/lr.xml Fri Jan 22 14:32:45 2021 +0000 @@ -9,7 +9,7 @@ <command detect_errors="exit_code"><![CDATA[ ## initialize @BAM@ - + ## run delly lr ## generic options @@ -26,99 +26,97 @@ --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 -#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' +## input +#for $i, $current in enumerate($input) + 'input_${i}.bam' #end for ## postprocessing @LOG@ +@DUMP@ @VCF@ -@DUMP@ ]]></command> <inputs> - <expand macro="samples"/> + <expand macro="input" format="bam" multiple="true" label="Select input file(s)"/> <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> + <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="1" label="Set minimum mapping quality"/> + <param argument="--mapqual" type="integer" value="10" label="Set minimum mapping quality"/> <expand macro="minclip"/> <expand macro="mincliquesize"/> - <expand macro="minrefsep" defaut="30"/> - <expand macro="maxreadsep" defaut="75"/> + <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="vcffile"/> <expand macro="genoqual"/> </section> - <section name="oo" title="Output options"> + <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="vcf">VCF</option> + <option value="log">Log</option> <option value="dump">SV-reads</option> - <option value="log">Log</option> + <option value="vcf">VCF</option> </param> </section> </inputs> <outputs> - <expand macro="vcf"/> <expand macro="bcf"/> <expand macro="dump"/> <expand macro="log"/> + <expand macro="vcf"/> </outputs> <tests> - <!-- no test implemented for parameter vcffile --> - <!-- #1 default, single --> <test expect_num_outputs="2"> - <param name="samples" value="normal.bam"/> + <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="1184" 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_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"/> + <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_vcf"> - <assert_contents> - <has_size value="3667" delta="10"/> - </assert_contents> - </output> <output name="out_bcf"> <assert_contents> <has_size value="1189" delta="10"/> @@ -129,10 +127,15 @@ <has_text_matching expression=".+Done.+"/> </assert_contents> </output> + <output name="out_vcf"> + <assert_contents> + <has_size value="3667" delta="10"/> + </assert_contents> + </output> </test> <!-- #3 --> <test expect_num_outputs="4"> - <param name="samples" value="normal.bam"/> + <param name="input" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="exclude" value="exclude.tsv"/> @@ -140,11 +143,6 @@ <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"/> @@ -160,10 +158,15 @@ <has_text_matching expression=".+Done.+"/> </assert_contents> </output> + <output name="out_vcf"> + <assert_contents> + <has_size value="3661" delta="10"/> + </assert_contents> + </output> </test> <!-- #4 --> <test expect_num_outputs="4"> - <param name="samples" value="normal.bam"/> + <param name="input" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="svtype" value="DEL"/> @@ -178,6 +181,11 @@ <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> @@ -189,12 +197,6 @@ <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"/> @@ -205,10 +207,16 @@ <has_text_matching expression=".+"/> </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> </test> <!-- #5 --> <test expect_num_outputs="1"> - <param name="samples" value="normal.bam"/> + <param name="input" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="svtype" value="INS"/> @@ -225,7 +233,7 @@ </test> <!-- #6 --> <test expect_num_outputs="1"> - <param name="samples" value="normal.bam"/> + <param name="input" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="svtype" value="DUP"/> @@ -241,7 +249,7 @@ </test> <!-- #7 --> <test expect_num_outputs="1"> - <param name="samples" value="normal.bam"/> + <param name="input" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="svtype" value="INV"/> @@ -257,7 +265,7 @@ </test> <!-- #8 --> <test expect_num_outputs="1"> - <param name="samples" value="normal.bam"/> + <param name="input" value="normal.bam"/> <section name="generic"> <param name="genome" value="genome.fasta"/> <param name="svtype" value="BND"/> @@ -279,15 +287,13 @@ @WID@ -Delly *long-read (lr)* uses the long-read SV discovery mode. - **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. Additionally a VCF/BCF file for genotyping can be applied. +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 is provided. +The output is available in BCF and VCF format. Additionally an output file for SV-reads and a log file are provided. .. class:: infomark