Mercurial > repos > artbio > lumpy_sv
diff lumpy.xml @ 0:796552c157de draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
| author | artbio |
|---|---|
| date | Mon, 24 Jul 2017 08:03:17 -0400 |
| parents | |
| children | 1ed8619a5611 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lumpy.xml Mon Jul 24 08:03:17 2017 -0400 @@ -0,0 +1,284 @@ +<tool id="lumpy" name="lumpy-sv" version="1.0.0"> + <description>find structural variants</description> + <requirements> + <requirement type="package" version="0.2.13">lumpy-sv</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> + <requirement type="package" version="1.11.2=py27_0">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 $seq_method.seq_method_list == "paired-end": + samtools view -u -F 1294 '$one_sample_bam' | samtools sort -O bam -o input.discordants.bam && + samtools view -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam && + samtools view '$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.evidence $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 $seq_method.seq_method_list == "single-read": + samtools view -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam && + lumpy $seq_method.additional_params.evidence $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 $seq_method.seq_method_list == "paired-end": + samtools view -u -F 1294 '$sample_a_bam' | samtools sort -O bam -o input.discordants.bam && + samtools view -u -F 1294 '$sample_b_bam' | samtools sort -O bam -o input.B.discordants.bam && + samtools view -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam && + samtools view -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.B.splitters.bam && + samtools view '$sample_a_bam' + |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandevA.txt && + samtools view '$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.evidence $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 $seq_method.seq_method_list == "single-read": + samtools view -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam && + samtools view -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.B.splitters.bam && + lumpy $seq_method.additional_params.evidence $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"/> + <param name="evidence" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="true" label="show evidence for each call"/> + </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"/> + <param name="evidence" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="show evidence for each call"/> + </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 on ${on_string}: 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 on ${on_string}: Fragment 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}: Split 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}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.B.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> + <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> + <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="evidence" value="true" /> + <param name="probability_curve" value="true" /> + <output name="vcf_call" file="output_extended.vcf" ftype="vcf" compare="sim_size"/> + </test> + <test> + <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>