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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit 37c0f0938a5cad74c954a89827a6a08bbbb81cb0
| author | artbio |
|---|---|
| date | Mon, 08 Jul 2024 22:23:10 +0000 |
| parents | 6ae3a402b9af |
| children |
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<tool id="lumpy" name="lumpy-sv" version="1.3"> <description>find structural variants</description> <requirements> <requirement type="package" version="0.3.1">lumpy-sv</requirement> <requirement type="package" version="1.18">samtools</requirement> <requirement type="package" version="1.16.5">numpy</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command detect_errors="exit_code"><![CDATA[ #import re #set one_sample_bam = re.sub('[^\w\-]', '_', str($analysis_type.input_file.element_identifier)) #if $analysis_type.analysis_type_list == "one_sample": ln -f -s '$analysis_type.input_file' '$one_sample_bam' && #else: #set sample_a_bam = re.sub('[^\w\-]', '_', str($analysis_type.input_file.element_identifier)) #set sample_b_bam = re.sub('[^\w\-]', '_', str($analysis_type.input_fileB.element_identifier)) #if $sample_a_bam == $sample_b_bam: #set sample_a_bam = "%s_a" % str($sample_a_bam) #set sample_b_bam = "%s_b" % str($sample_b_bam) #end if ln -f -s '$analysis_type.input_file' '$sample_a_bam' && ln -f -s '$analysis_type.input_fileB' '$sample_b_bam' && #end if #if $analysis_type.analysis_type_list == "one_sample": #if $seq_method.seq_method_list == "paired-end": samtools view -@ \${GALAXY_SLOTS:-4} -u -F 1294 '$one_sample_bam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.discordants.bam && samtools view -@ \${GALAXY_SLOTS:-4} -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam && samtools view -@ \${GALAXY_SLOTS:-4} '$one_sample_bam' |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && lumpy $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt #if $output_format == "BEDPE": -b #end if -pe id:'$one_sample_bam',bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:'$one_sample_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call' #elif $seq_method.seq_method_list == "single-read": samtools view -@ \${GALAXY_SLOTS:-4} -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam && lumpy $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt #if $output_format == "BEDPE": -b #end if -sr id:'$one_sample_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call' #end if #else: #if $seq_method.seq_method_list == "paired-end": samtools view -@ \${GALAXY_SLOTS:-4} -u -F 1294 '$sample_a_bam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.discordants.bam && samtools view -@ \${GALAXY_SLOTS:-4} -u -F 1294 '$sample_b_bam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.B.discordants.bam && samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam && samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.B.splitters.bam && samtools view -@ \${GALAXY_SLOTS:-4} '$sample_a_bam' |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandevA.txt && samtools view -@ \${GALAXY_SLOTS:-4} '$sample_b_bam' |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt && meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) && meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && lumpy $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt #if $output_format == "BEDPE": -b #end if -pe id:inputA.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$analysis_type.readLengthB,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:inputA.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call' #elif $seq_method.seq_method_list == "single-read": samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam && samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.B.splitters.bam && lumpy $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt #if $output_format == "BEDPE": -b #end if -sr id:'$sample_a_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold -sr id:'$sample_b_bam',bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call' #end if #end if ]]></command> <!-- basic error handling --> <inputs> <conditional name="analysis_type"> <param help="Single or paired conditions (eg tumor vs normal)" label="Input(s)" name="analysis_type_list" type="select"> <option selected="True" value="one_sample">One Sample</option> <option value="two_sample">Two samples</option> </param> <when value="one_sample"> <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/> <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" /> </when> <when value="two_sample"> <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/> <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" /> <param format="bam" name="input_fileB" type="data" label="One BAM alignment file produced by BWA-mem"/> <param name="readLengthB" value="151" type="integer" label="read length" help="e.g. 151 nt" /> </when> </conditional> <conditional name="seq_method"> <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select"> <option selected="True" value="paired-end">Paired-end sequencing</option> <option value="single-read">Single-read sequencing</option> </param> <when value="paired-end"> <section name="additional_params" title="Additional Options" expanded="False"> <param name="samplingValue" value="100000" type="integer" label="number of reads to compute mean and stdev of read length" help="e.g. 10000" /> <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" /> <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" /> <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" /> <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" /> <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" /> <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" /> <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" /> <param name="probability_curve" argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="true" label="output probability curve for each variant"/> </section> </when> <when value="single-read"> <section name="additional_params" title="Additional Options" expanded="False"> <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" /> <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" /> <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" /> <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" /> <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" /> <param name="probability_curve" argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="false" label="output probability curve for each variant"/> </section> </when> </conditional> <param help="get variant calling in vcf or BEDPE format" label="variant calling format" name="output_format" type="select"> <option selected="True" value="vcf">vcf</option> <option value="BEDPE">BEDPE</option> </param> </inputs> <outputs> <data format="tabular" name="histogram" label="Lumpy-sv: Fragment size distribution" from_work_dir="input.lib.histo"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> <data format="tabular" name="histogramB" label="Lumpy-sv: FragmentB size distribution" from_work_dir="input.B.lib.histo"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> <data format="bam" name="splits" label="Lumpy on ${on_string}: Split Reads (Bam format)" from_work_dir="input.splitters.bam"/> <data format="bam" name="splitsB" label="Lumpy on ${on_string}: SplitB Reads (Bam format)" from_work_dir="input.B.splitters.bam"> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.bam"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: DiscordantB Pairs (Bam format)" from_work_dir="input.B.discordants.bam"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> <data format="vcf" name="vcf_call" label="Lumpy Variant Calling"> <change_format> <when format="tabular" input="output_format" value="BEDPE" /> </change_format> </data> </outputs> <tests> <test expect_num_outputs="7"> <param name="analysis_type_list" value="two_sample" /> <param name="input_file" value="sample_Del.bam" ftype="bam"/> <param name="input_fileB" value="sample_cle.bam" ftype="bam"/> <param name="seq_method_list" value="paired-end" /> <param name="mw" value="4"/> <param name="tt" value="0"/> <param name="back_distance" value="10"/> <param name="weight" value="1" /> <param name="min_mapping_threshold" value="20" /> <output name="vcf_call" file="output_two.paired_end.vcf" ftype="vcf"/> </test> <test expect_num_outputs="2"> <param name="analysis_type_list" value="one_sample" /> <param name="input_file" value="sr.input.bam" ftype="bam"/> <param name="seq_method_list" value="single-read" /> <param name="mw" value="4"/> <param name="tt" value="0"/> <param name="back_distance" value="10"/> <param name="weight" value="1" /> <param name="min_mapping_threshold" value="20" /> <output name="vcf_call" file="output.vcf" ftype="vcf"/> </test> <test expect_num_outputs="2"> <param name="analysis_type_list" value="one_sample" /> <param name="input_file" value="sr.input.bam" ftype="bam"/> <param name="seq_method_list" value="single-read" /> <param name="mw" value="4"/> <param name="tt" value="0"/> <param name="back_distance" value="10"/> <param name="weight" value="1" /> <param name="min_mapping_threshold" value="20" /> <param name="probability_curve" value="true" /> <output name="vcf_call" file="output_extended.vcf" ftype="vcf" compare="sim_size"/> </test> <test expect_num_outputs="3"> <param name="analysis_type_list" value="two_sample" /> <param name="input_file" value="sr.input.bam" ftype="bam"/> <param name="input_fileB" value="sr.input.bam" ftype="bam"/> <param name="seq_method_list" value="single-read" /> <param name="mw" value="4"/> <param name="tt" value="0"/> <param name="back_distance" value="10"/> <param name="weight" value="1" /> <param name="min_mapping_threshold" value="20" /> <output name="vcf_call" file="output_two.vcf" ftype="vcf"/> </test> </tests> <help> **Input(s)** *One sample* : lumpy search structural variations inside a single sequencing dataset *Two samples*: lumpy search structural variations inside and across two sequencing datasets from two samples Analysis of sample replicates is not implemented yet in this wrapper *BAM files*: Only BAM alignments produced by BWA-mem have been tested with this tool **Sequencing method** *Paired-end sequencing*: Both ends of library fragments have been sequenced, resulting in two paired sequencing datasets *Single-read sequencing*: Only one end of library fragment has been sequenced, resulting in a single sequencing dataset. Under these conditions, evidences of structural variation are obtained only from splited read alignments *Read length*: The length of the sequencing reads in the library. This information is required only for paired-end sequencing data *Additional options*: refer to lumpy-sv_ documentation and the publication (doi 10.1186/gb-2014-15-6-r84) **lumpy-sv manual** Read the lumpy-sv_ documentation for details on using lumpy. .. _lumpy-sv: https://github.com/arq5x/lumpy-sv **lumpy options** v 0.2.13 Author: Ryan Layer (rl6sf@virginia.edu) Summary: Find structural variations in various signals. Options:: <![CDATA[ -g Genome file (defines chromosome order) -e Show evidence for each call -w File read windows size (default 1000000) -mw minimum weight for a call -msw minimum per-sample weight for a call -tt trim threshold -x exclude file bed file -t temp file prefix, must be to a writeable directory -P output probability curve for each variant -b output BEDPE instead of VCF -sr bam_file:<file name>, id:<sample name>, back_distance:<distance>, min_mapping_threshold:<mapping quality>, weight:<sample weight>, min_clip:<minimum clip length>, read_group:<string> -pe bam_file:<file name>, id:<sample name>, histo_file:<file name>, mean:<value>, stdev:<value>, read_length:<length>, min_non_overlap:<length>, discordant_z:<z value>, back_distance:<distance>, min_mapping_threshold:<mapping quality>, weight:<sample weight>, read_group:<string> -bedpe bedpe_file:<bedpe file>, id:<sample name>, weight:<sample weight> ]]> </help> <citations> <citation type="doi">10.1186/gb-2014-15-6-r84</citation> </citations> </tool>