Mercurial > repos > iuc > delly_call
changeset 4:4869d7517a51 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d76130cdcb21f0390b4e68e733d38575fd5cc6c7"
| author | iuc |
|---|---|
| date | Tue, 14 Dec 2021 19:02:43 +0000 |
| parents | f0a5257823ba |
| children | 29f28384af45 |
| files | cnv.xml.orig macros.xml macros.xml.orig merge.xml.orig |
| diffstat | 4 files changed, 2 insertions(+), 550 deletions(-) [+] |
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--- a/cnv.xml.orig Tue Aug 31 07:59:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,207 +0,0 @@ -<?xml version="1.0"?> -<<<<<<< HEAD:tools/delly/cnv.xml -<tool id="delly_cnv" name="Delly cnv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> - <description>discover and genotype copy-number variants</description> -======= -<tool id="delly_rd" name="Delly read-depth (rd)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> - <description>normalization on read-depth profiles</description> - <expand macro="bio_tools"/> ->>>>>>> 20ed9dd6f (add bio.tools ID):tools/delly/rd.xml - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="version_command"/> - <command detect_errors="exit_code"><![CDATA[ -## run -delly cnv -## generic options ---genome '$generic.genome' ---quality '$generic.quality' ---mappability '$generic.mappability' ---ploidy $generic.ploidy ---outfile 'result.bcf' ---covfile 'result.gz' -## cnv calling options ---sdrd $cnv.sdrd ---cn-offset $cnv.cnoffset ---cnv-size $cnv.cnvsize -#if $cnv.svfile - --svfile $cnv.svfile -#end if -#if $cnv.vcffile - --vcffile '$cnv.vcffile' -#end if -$cnv.segmentation -## read-depth window options ---window-size $read.windowsize ---window-offset $read.windowoffset -#if $read.bedintervals - --bed-intervals '$read.bedintervals' -#end if ---fraction-window $read.fractionwindow -$read.adaptivewindowing -## gc fragment normalization options ---scan-window $gc.scanwindow ---fraction-unique $gc.fractionunique -#if $gc.scanregions - --scan-regions '$gc.scanregions' -#end if ---mad-cutoff $gc.madcutoff ---percentile $gc.percentile -$gc.nowindowselection -## input -'$input' - -## postprocessing -@LOG@ - ]]></command> - <inputs> - <expand macro="input" format="bam" label="Select input file"/> - <section name="generic" title="Generic options" expanded="true"> - <expand macro="genome"/> - <param argument="--quality" type="integer" value="10" label="Set minimum mapping quality"/> - <param argument="--mappability" type="data" format="fasta" label="Select mappability map file"/> - <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/> - </section> - <section name="cnv" title="CNV calling options" expanded="true"> - <param argument="--sdrd" type="integer" value="2" label="Set minimum SD read-depth shift"/> - <expand macro="cnoffset" default="0.1"/> - <param name="cnvsize" type="integer" value="1000" label="Set minimum CNV size" help="(--cnv-size)"/> - <param argument="--svfile" type="data" format="bcf" optional="true" label="Select delly SV file for breakpoint refinement"/> <!-- filetype sv.bcf not supported by galaxy --> - <expand macro="vcffile"/> - <param argument="--segmentation" type="boolean" truevalue="--segmentation" falsevalue="" label="Use copy-number segmentation?"/> - </section> - <section name="read" title="Read-depth window options" expanded="true"> - <param name="windowsize" type="integer" value="10000" label="Set window size" help="(--window-size)"/> - <param name="windowoffset" type="integer" value="10000" label="Set window offset" help="(--window-offset)"/> - <param name="bedintervals" type="data" format="bed" optional="true" label="Select input BED file" help="(--bed-intervals)"/> - <param name="fractionwindow" type="float" min="0.0" max="1.0" value="0.25" label="Set minimum callable window fraction" help="(--fraction-window)"/> - <param name="adaptivewindowing" type="boolean" truevalue="-a" falsevalue="" label="Use mappable bases for window size?" help="(--adaptive-windowing)"/> - </section> - <section name="gc" title="GC fragment normalization options" expanded="true"> - <param name="scanwindow" type="integer" value="10000" label="Set scan window size" help="(--scan-window)"/> - <param name="fractionunique" type="float" min="0.0" max="1.0" value="0.8" label="Set uniqueness filter for scan windows" help="(--fraction-unique)"/> - <param name="scanregions" type="data" format="bed" optional="true" label="Select file with scanning regions" help="(--scan-regions)"/> - <param name="madcutoff" type="integer" value="3" label="Set count cutoff" help="(median + 3 * mad) (--mad-cutoff)"/> - <param argument="--percentile" type="float" min="0.0" max="1.0" value="0.0005" label="Set threshold for excluding extreme GC fraction"/> - <param name="nowindowselection" type="boolean" truevalue="-n" falsevalue="" label="Skip scan window selection?" help="(--no-window-selection)"/> - </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="cnv" selected="true">CNV</option> - <option value="coverage">Coverage</option> - <option value="log">Log</option> - </param> - </section> - </inputs> - <outputs> - <data name="out_cnv" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: CNV"> - <filter>'cnv' in oo['out']</filter> - </data> - <data name="out_coverage" format="tabular.gz" from_work_dir="result.gz" label="${tool.name} on ${on_string}: Coverage"> - <filter>'coverage' in oo['out']</filter> - </data> - <expand macro="log"/> - </outputs> - <tests> - <!-- no test implemented for vcffile, svfile, bed-intervals, scanregions --> - - <!-- #1 default; test data to small, results are empty --> - <test expect_num_outputs="3"> - <param name="input" value="normal.bam"/> - <section name="generic"> - <param name="genome" value="genome.fasta"/> - <param name="mappability" value="map.fasta"/> - </section> - <section name="oo"> - <param name="out" value="cnv,coverage,log"/> - </section> - <output name="out_cnv"> - <assert_contents> - <has_size value="0"/> - </assert_contents> - </output> - <output name="out_coverage"> - <assert_contents> - <has_size value="0"/> - </assert_contents> - </output> - <output name="out_log"> - <assert_contents> - <has_text_matching expression=".+Scanning Windows"/> - <has_line line="***************************************************"/> - </assert_contents> - </output> - </test> - <!-- #2 --> - <test expect_num_outputs="3"> - <param name="input" value="normal.bam"/> - <section name="generic"> - <param name="genome" value="genome.fasta"/> - <param name="quality" value="11"/> - <param name="mappability" value="map.fasta"/> - <param name="ploidy" value="3"/> - </section> - <section name="cnv"> - <param name="sdrd" value="3"/> - <param name="cnoffset" value="0.2"/> - <param name="cnvsize" value="1001"/> - <param name="segmentation" value="true"/> - </section> - <section name="read"> - <param name="windowsize" value="10001"/> - <param name="windowoffset" value="9999"/> - <param name="fractionwindow" value="0.24"/> - <param name="adaptivewindowing" value="true"/> - </section> - <section name="gc"> - <param name="scanwindow" value="10001"/> - <param name="fractionunique" value="0.79"/> - <param name="madcutoff" value="2"/> - <param name="percentile" value="0.0006"/> - <param name="nowindowselection" value="true"/> - </section> - <section name="oo"> - <param name="out" value="cnv,coverage,log"/> - </section> - <output name="out_cnv"> - <assert_contents> - <has_size value="700" delta="10"/> - </assert_contents> - </output> - <output name="out_coverage"> - <assert_contents> - <has_size value="61"/> - </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 *cnv* requires are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which is available `here <https://gear.embl.de/data/delly/>`_. Intervals (BED), scanning regions (BED) and a delly SV file for breakpoint refinement (BCF) can be provided optionally. - -**Output** - -CNV (BCF) and coverage (compressed tabular) files are created. - -.. class:: infomark - -**References** - -@REFERENCES@ - ]]></help> - <expand macro="citations"/> -</tool> \ No newline at end of file
--- a/macros.xml Tue Aug 31 07:59:23 2021 +0000 +++ b/macros.xml Tue Dec 14 19:02:43 2021 +0000 @@ -1,11 +1,11 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.8.7</token> + <token name="@TOOL_VERSION@">0.9.1</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">delly</requirement> - <requirement type="package" version="1.10.2">bcftools</requirement> + <requirement type="package" version="1.12">bcftools</requirement> </requirements> </xml> <xml name="version_command">
--- a/macros.xml.orig Tue Aug 31 07:59:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,162 +0,0 @@ -<?xml version="1.0"?> -<macros> - <token name="@TOOL_VERSION@">0.8.7</token> - <token name="@VERSION_SUFFIX@">0</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">delly</requirement> - <requirement type="package" version="1.10.2">bcftools</requirement> - </requirements> - </xml> - <xml name="version_command"> - <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command> - </xml> - <xml name="citations"> - <citations> - <citation type="doi">10.1093/bioinformatics/bts378</citation> - </citations> - </xml> -<<<<<<< HEAD - - <!-- command --> -======= - <xml name="bio_tools"> - <xrefs> - <xref type='bio.tools'>delly2</xref> - </xrefs> - </xml> - <!-- - command - --> ->>>>>>> 20ed9dd6f (add bio.tools ID) - - <token name="@BAM@"><![CDATA[ -#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[ -#if 'dump' in $oo.out - && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.' -#end if - ]]></token> - <token name="@LOG@"><![CDATA[ -#if 'log' in $oo.out - |& tee '$out_log' -#end if - ]]></token> - <token name="@VCF@"><![CDATA[ -#if 'vcf' in $oo.out - && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.' -#end if - ]]></token> - - <!-- 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 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="mincliquesize"> - <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/> - </xml> - <xml name="minrefsep" token_default=""> - <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/> - </xml> - <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="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="INV">Inversion (INV)</option> - <option value="BND">Translocation (BND)</option> - </param> - </xml> - <xml name="vcffile"> - <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/> - </xml> - - <!-- 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 ${on_string}: Result (VCF)"> - <filter>'vcf' in oo['out']</filter> - </data> - </xml> - <xml name="dump"> - <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads"> - <filter>'dump' in oo['out']</filter> - </data> - </xml> - <xml name="log"> - <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> - <filter>'log' in oo['out']</filter> - </data> - </xml> - - <!-- 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>`_. - ]]></token> -</macros> \ No newline at end of file
--- a/merge.xml.orig Tue Aug 31 07:59:23 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,179 +0,0 @@ -<?xml version="1.0"?> -<tool id="delly_merge" name="Delly merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> -<<<<<<< HEAD - <description>structural variants across/within BCF/VCF file(s)</description> -======= - <description>structural variants across/within VCF/BCF file(s)</description> - <expand macro="bio_tools"/> ->>>>>>> 20ed9dd6f (add bio.tools ID) - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="version_command"/> - <command detect_errors="exit_code"><![CDATA[ -## initialize -#for $i, $current in enumerate($input) - #if $current.is_of_type('vcf') - bcftools view -Ob '$current' > 'input_${i}.bcf.gz' && - bcftools index 'input_${i}.bcf.gz' && - #else - ln -s '${current}' 'input_${i}.bcf.gz' && - ln -s '${current.metadata.bcf_index}' 'input_${i}.bcf.gz.csi' && - #end if -#end for - -## run -delly merge -## generic options ---outfile 'result.bcf' ---chunks $generic.chunks ---vaf $generic.vaf ---coverage $generic.coverage ---minsize $generic.minsize ---maxsize $generic.maxsize -$generic.cnvmode -$generic.precise -$generic.pass -## overlap options ---bp-offset $overlap.bpoffset ---rec-overlap $overlap.recoverlap -## input -#for $i, $current in enumerate($input) - 'input_${i}.bcf.gz' -#end for - -## postprocessing -@LOG@ -@VCF@ - ]]></command> - <inputs> - <expand macro="input" format="bcf,vcf" multiple="true" label="Select input files"/> - <section name="generic" title="Generic options" expanded="true"> - <param argument="--chunks" type="integer" value="500" label="Set maximum chunk size to merge groups of BCF files"/> - <param argument="--vaf" type="float" value="0.15" min="0.0" max="1.0" label="Set minimum fractional ALT support"/> - <expand macro="coverage" label="Set minimum coverage"/> - <expand macro="minsize" default="0" label="Set minimum SV size"/> - <expand macro="maxsize" default="1000000" label="Set maximum SV size"/> - <param argument="--cnvmode" type="boolean" truevalue="--cnvmode" falsevalue="" label="Merge Delly CNV files?"/> - <param argument="--precise" type="boolean" truevalue="--precise" falsevalue="" label="Filter sites for PRECISE?"/> - <expand macro="pass"/> - </section> - <section name="overlap" title="Overlap options" expanded="true"> - <param name="bpoffset" type="integer" value="1000" label="Set maximum breakpoint offset" help="(--bp-offset)"/> - <param name="recoverlap" type="float" value="0.8" label="Set minimum reciprocal overlap" help="(--rec-overlap)"/> - </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="vcf">VCF</option> - </param> - </section> - </inputs> - <outputs> - <expand macro="bcf"/> - <expand macro="log"/> - <expand macro="vcf"/> - </outputs> - <tests> - <!-- #1 bcf, default --> - <test expect_num_outputs="2"> - <param name="input" value="call_1.bcf.gz,call_2.bcf.gz"/> - <section name="oo"> - <param name="out" value="vcf,bcf"/> - </section> - <output name="out_bcf"> - <assert_contents> - <has_size value="1851" delta="10"/> - </assert_contents> - </output> - <output name="out_vcf"> - <assert_contents> - <has_n_lines n="128"/> - <has_line line="##fileformat=VCFv4.2"/> - <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"/> - </assert_contents> - </output> - </test> - <!-- #2 bcf --> - <test expect_num_outputs="3"> - <param name="input" value="call_1.bcf.gz,call_2.bcf.gz"/> - <section name="generic"> - <param name="chunks" value="500"/> - <param name="vaf" value="0.16"/> - <param name="coverage" value="10"/> - <param name="minsize" value="0"/> - <param name="maxsize" value="1000000"/> - <param name="cnvmode" value="true"/> - <param name="precise" value="true"/> - <param name="pass" value="true"/> - </section> - <section name="overlap"> - <param name="bp-offset" value="1000"/> - <param name="rec-overlap" value="0.79"/> - </section> - <section name="oo"> - <param name="out" value="vcf,bcf,log"/> - </section> - <output name="out_bcf"> - <assert_contents> - <has_size value="1021" 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="108"/> - <has_line line="##fileformat=VCFv4.2"/> - <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"/> - </assert_contents> - </output> - </test> - <!-- #3 vcf, default --> - <test expect_num_outputs="2"> - <param name="input" value="call_1.vcf.gz,call_2.vcf.gz"/> - <section name="oo"> - <param name="out" value="vcf,bcf"/> - </section> - <output name="out_bcf"> - <assert_contents> - <has_size value="1851" delta="10"/> - </assert_contents> - </output> - <output name="out_vcf"> - <assert_contents> - <has_n_lines n="128"/> - <has_line line="##fileformat=VCFv4.2"/> - <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO"/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[ -.. class:: infomark - -**What it does** - -@WID@ - -**Input** - -Delly *merge* requires BCF or VCF files. - -**Output** - -A single file in BCF/VCF format. Additionally a log file is provided. - -.. class:: infomark - -**References** - -@REFERENCES@ - ]]></help> - <expand macro="citations"/> -</tool> \ No newline at end of file