| Previous changeset 1:d5124d5c8131 (2020-10-29) Next changeset 3:d30785dbe6b7 (2021-12-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a" |
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modified:
lr.xml macros.xml |
| b |
| diff -r d5124d5c8131 -r ceda4714f3a1 lr.xml --- a/lr.xml Thu Oct 29 20:51:54 2020 +0000 +++ b/lr.xml Fri Jan 22 14:32:45 2021 +0000 |
| [ |
| b'@@ -9,7 +9,7 @@\n <command detect_errors="exit_code"><![CDATA[\n ## initialize\n @BAM@\n- \n+\n ## run\n delly lr\n ## generic options\n@@ -26,99 +26,97 @@\n --min-clique-size $discovery.mincliquesize\n --minrefsep $discovery.minrefsep\n --maxreadsep $discovery.maxreadsep\n+## consensus options\n+--max-reads $consensus.maxreads\n+--flank-size $consensus.flanksize\n+--flank-quality $consensus.flankquality\n ## genotyping options\n-#if $genotyping.vcffile\n- --vcffile \'$genotyping.vcffile\'\n-#end if\n --geno-qual $genotyping.genoqual\n #if \'dump\' in $oo.out\n --dump \'dump.tsv.gz\'\n #end if\n-## samples\n-#for $i, $current in enumerate($samples)\n- \'sample_${i}.bam\'\n+## input\n+#for $i, $current in enumerate($input)\n+ \'input_${i}.bam\'\n #end for\n \n ## postprocessing\n @LOG@\n+@DUMP@\n @VCF@\n-@DUMP@\n ]]></command>\n <inputs>\n- <expand macro="samples"/>\n+ <expand macro="input" format="bam" multiple="true" label="Select input file(s)"/>\n <section name="generic" title="Generic options" expanded="true">\n- <expand macro="genome"/>\n <expand macro="svtype"/>\n- <expand macro="exclude"/>\n <param argument="--technology" type="select" label="Select sequencing technology">\n <option value="ont" selected="true">Oxford Nanopore (ont)</option>\n- <option value="pb">Pacbio (pb)</option>\n+ <option value="pb">PacBio (pb)</option>\n </param>\n+ <expand macro="genome"/>\n+ <expand macro="exclude"/>\n </section>\n <section name="discovery" title="Discovery options" expanded="true">\n- <param argument="--mapqual" type="integer" value="1" label="Set minimum mapping quality"/>\n+ <param argument="--mapqual" type="integer" value="10" label="Set minimum mapping quality"/>\n <expand macro="minclip"/>\n <expand macro="mincliquesize"/>\n- <expand macro="minrefsep" defaut="30"/>\n- <expand macro="maxreadsep" defaut="75"/>\n+ <expand macro="minrefsep" default="30"/>\n+ <expand macro="maxreadsep" default="75"/>\n+ </section>\n+ <section name="consensus" title="Consensus options" expanded="true">\n+ <param name="maxreads" type="integer" value="5" label="Set maximum reads for consensus computation" help="(--max-reads)"/>\n+ <param name="flanksize" type="integer" value="400" label="Set minimum flank size" help="(--flank-size)"/>\n+ <param name="flankquality" type="float" min="0.0" max="1.0" value="0.9" label="Set minimum flank quality" help="(--flank-quality)"/>\n </section>\n <section name="genotyping" title="Genotyping options" expanded="true">\n- <expand macro="vcffile"/>\n <expand macro="genoqual"/>\n </section>\n- <section name="oo" title="Output options">\n+ <section name="oo" title="Output options" expanded="true">\n <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">\n <option value="bcf" selected="true">BCF</option>\n- <option value="vcf">VCF</option>\n+ <option value="log">Log</option>\n <option value="dump">SV-reads</option>\n- <option value="log">Log</option>\n+ <option value="vcf">VCF</option>\n </param>\n </section>\n </inputs>\n <outputs>\n- <expand macro="vcf"/>\n <expand macro="bcf"/>\n <expand macro="dump"/>\n <expand macro="log"/>\n+ <expand macro="vcf"/>\n </outputs>\n <tests>\n- <!-- no test implemented for parameter vcffile -->\n-\n <!-- #1 default, single -->\n <test expect_num_outputs="2">\n- <param name="samples" value="normal.bam"/>\n+ <param name="input" value="normal.bam"/>\n <section name="generic">\n <param name="genome" value="genome.fasta"/>'..b'num_outputs="4">\n- <param name="samples" value="normal.bam"/>\n+ <param name="input" value="normal.bam"/>\n <section name="generic">\n <param name="genome" value="genome.fasta"/>\n <param name="svtype" value="DEL"/>\n@@ -178,6 +181,11 @@\n <param name="minrefsep" value="24"/>\n <param name="maxreadsep" value="39"/>\n </section>\n+ <section name="consensus">\n+ <param name="maxreads" value="6"/>\n+ <param name="flanksize" value="399"/>\n+ <param name="flankquality" value="0.91"/>\n+ </section>\n <section name="genotyping">\n <param name="genoqual" value="4"/>\n </section>\n@@ -189,12 +197,6 @@\n <has_size value="1182" delta="10"/>\n </assert_contents>\n </output>\n- <output name="out_vcf">\n- <assert_contents>\n- <has_size value="3661" delta="10"/>\n- <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/>\n- </assert_contents>\n- </output>\n <output name="out_dump">\n <assert_contents>\n <has_size value="0"/>\n@@ -205,10 +207,16 @@\n <has_text_matching expression=".+"/>\n </assert_contents>\n </output>\n+ <output name="out_vcf">\n+ <assert_contents>\n+ <has_size value="3661" delta="10"/>\n+ <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/>\n+ </assert_contents>\n+ </output>\n </test>\n <!-- #5 -->\n <test expect_num_outputs="1">\n- <param name="samples" value="normal.bam"/>\n+ <param name="input" value="normal.bam"/>\n <section name="generic">\n <param name="genome" value="genome.fasta"/>\n <param name="svtype" value="INS"/>\n@@ -225,7 +233,7 @@\n </test>\n <!-- #6 -->\n <test expect_num_outputs="1">\n- <param name="samples" value="normal.bam"/>\n+ <param name="input" value="normal.bam"/>\n <section name="generic">\n <param name="genome" value="genome.fasta"/>\n <param name="svtype" value="DUP"/>\n@@ -241,7 +249,7 @@\n </test>\n <!-- #7 -->\n <test expect_num_outputs="1">\n- <param name="samples" value="normal.bam"/>\n+ <param name="input" value="normal.bam"/>\n <section name="generic">\n <param name="genome" value="genome.fasta"/>\n <param name="svtype" value="INV"/>\n@@ -257,7 +265,7 @@\n </test>\n <!-- #8 -->\n <test expect_num_outputs="1">\n- <param name="samples" value="normal.bam"/>\n+ <param name="input" value="normal.bam"/>\n <section name="generic">\n <param name="genome" value="genome.fasta"/>\n <param name="svtype" value="BND"/>\n@@ -279,15 +287,13 @@\n \n @WID@\n \n-Delly *long-read (lr)* uses the long-read SV discovery mode.\n-\n **Input**\n \n-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.\n+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.\n \n **Output**\n \n-The output is available in BCF and VCF format. Additionally an output file for SV-reads is provided.\n+The output is available in BCF and VCF format. Additionally an output file for SV-reads and a log file are provided.\n \n .. class:: infomark\n \n' |
| b |
| diff -r d5124d5c8131 -r ceda4714f3a1 macros.xml --- a/macros.xml Thu Oct 29 20:51:54 2020 +0000 +++ b/macros.xml Fri Jan 22 14:32:45 2021 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.8.5</token> + <token name="@TOOL_VERSION@">0.8.7</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> @@ -17,14 +17,12 @@ </citations> </xml> - <!-- - command - --> + <!-- command --> <token name="@BAM@"><![CDATA[ -#for $i, $current in enumerate($samples) - ln -s '${current}' 'sample_${i}.bam' && - ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' && +#for $i, $current in enumerate($input) + ln -s '${current}' 'input_${i}.bam' && + ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' && #end for ]]></token> <token name="@DUMP@"><![CDATA[ @@ -43,68 +41,79 @@ #end if ]]></token> - <!-- - input - --> + <!-- input --> + <xml name="cnoffset" token_default=""> + <param name="cnoffset" type="float" min="0.0" max="1.0" value="@DEFAULT@" label="Set minimum CN offset" help="(--cn-offset)"/> + </xml> + <xml name="coverage" token_label=""> + <param argument="--coverage" type="integer" value="10" label="@LABEL@"/> + </xml> <xml name="exclude"> <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/> </xml> <xml name="genome"> - <param argument="--genome" type="data" format="fasta" label="Select genome"/> + <param argument="--genome" type="data" format="fasta" label="Select genome file"/> </xml> <xml name="genoqual"> <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/> </xml> + <xml name="input" token_format="" token_multiple="false" token_label=""> + <param name="input" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/> + </xml> + <xml name="maxreadsep" token_default=""> + <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/> + </xml> + <xml name="maxsize" token_default="" token_label=""> + <param argument="--maxsize" type="integer" value="@DEFAULT@" label="@LABEL@"/> + </xml> <xml name="minclip"> <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/> </xml> - <xml name="maxreadsep" token_default="40"> - <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/> + <xml name="mincliquesize"> + <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/> </xml> - <xml name="maxsize" token_default="1000000"> - <param argument="--maxsize" type="integer" value="@DEFAULT@" label="Set maximum SV size"/> - </xml> - <xml name="mincliquesize"> - <param name="mincliquesize" type="integer" value="2" label="Set minimum min. PE/SR clique size" help="(--min-clique-size)"/> - </xml> - <xml name="minrefsep" token_default="25"> + <xml name="minrefsep" token_default=""> <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/> </xml> - <xml name="minsize"> - <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/> + <xml name="minsize" token_default="" token_label=""> + <param argument="--minsize" type="integer" value="@DEFAULT@" label="@LABEL@"/> + </xml> + <xml name="pass"> + <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> </xml> - <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)"> - <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/> + <xml name="ploidy"> + <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/> + </xml> + <xml name="samples"> + <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/> </xml> <xml name="svtype"> <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect"> <option value="ALL" selected="true">All types (ALL)</option> <option value="DEL">Deletion (DEL)</option> + <option value="DUP">Duplication (DUP)</option> <option value="INS">Insertion (INS)</option> - <option value="DUP">Duplication (DUP)</option> <option value="INV">Inversion (INV)</option> <option value="BND">Translocation (BND)</option> </param> </xml> <xml name="vcffile"> - <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/> + <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/> </xml> - <!-- - output - --> + <!-- output --> + <xml name="bcf"> + <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)"> + <filter>'bcf' in oo['out']</filter> + </data> + </xml> <xml name="vcf"> <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)"> <filter>'vcf' in oo['out']</filter> </data> </xml> - <xml name="bcf"> - <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)"> - <filter>'bcf' in oo['out']</filter> - </data> - </xml> <xml name="dump"> <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads"> <filter>'dump' in oo['out']</filter> @@ -116,12 +125,25 @@ </data> </xml> - <!-- - Help - --> + <!-- help --> <token name="@WID@"><![CDATA[ Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. + +Short-read SV calling + +- *call* to discover and genotype structural variants +- *merge* structural variants across VCF/BCF files and within a single VCF/BCF file +- *filter* somatic or germline structural variants + +Long-read SV calling + +- *lr* for long-read SV discovery + +Copy-number variant calling + +- *cnv* to discover and genotype copy-number variants +- *classify* somatic or germline copy-number variants ]]></token> <token name="@REFERENCES@"><![CDATA[ More information are available on `GitHub <https://github.com/dellytools/delly>`_. |