# HG changeset patch # User artbio # Date 1591698219 14400 # Node ID f55d45b0c6d1fb100fc4fddf401b1a7296f56b12 # Parent d09254e37c68fd4065c9ab0c7f01367c3f39d251 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416" diff -r d09254e37c68 -r f55d45b0c6d1 customConfigManta.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/customConfigManta.py Tue Jun 09 06:23:39 2020 -0400 @@ -0,0 +1,80 @@ +import argparse + + +def Parser(): + the_parser = argparse.ArgumentParser() + the_parser.add_argument( + '--minCandidateVariantSize', type=int, default=8, + help="Run Manta reporting for all SVs/indels at or above this size") + the_parser.add_argument( + '--rnaMinCandidateVariantSize', type=int, default=1000, + help="Separate option (to provide different default) used for \ + runs in RNA-mode") + the_parser.add_argument( + '--minEdgeObservations', type=int, default=3, + help="Remove all edges from the graph unless they're supported \ + by this many 'observations'") + the_parser.add_argument( + '--graphNodeMaxEdgeCount', type=int, default=10, + help="If both nodes of an edge have an edge count higher than this, \ + then skip evaluation of the edge") + the_parser.add_argument( + '--minCandidateSpanningCount', type=int, default=3, + help="Run discovery and candidate reporting for all SVs/indels with \ + at least this many spanning support observations") + the_parser.add_argument( + '--minScoredVariantSize', type=int, default=50, + help="After candidate identification, only score and report \ + SVs/indels at or above this size") + the_parser.add_argument( + '--minDiploidVariantScore', type=int, default=10, + help="minimum VCF QUAL score for a variant to be included in \ + the diploid vcf") + the_parser.add_argument( + '--minPassDiploidVariantScore', type=int, default=20, + help="VCF QUAL score below which a variant is marked as \ + filtered in the diploid vcf") + the_parser.add_argument( + '--minPassDiploidGTScore', type=int, default=15, + help="minimum genotype quality score below which single samples \ + are filtered for a variant in the diploid vcf") + the_parser.add_argument( + '--minSomaticScore', type=int, default=10, + help="minimum VCF QUAL score for a variant to be included in the \ + diploid vcf") + the_parser.add_argument( + '--minPassSomaticScore', type=int, default=30, + help="somatic quality scores below this level are filtered in the \ + somatic vcf") + the_parser.add_argument( + '--enableRemoteReadRetrievalForInsertionsInGermlineCallingModes', + type=int, default=1, + help="includes tumor-normal subtraction and tumor-only calling") + the_parser.add_argument( + '--enableRemoteReadRetrievalForInsertionsInCancerCallingModes', + type=int, default=0, + help="GermlineCallingModes includes all other calling modes") + the_parser.add_argument( + '--useOverlapPairEvidence', type=int, default=0, + help="Set 1 if an overlapping read pair will be considered as \ + evidence. Set to 0 to skip overlapping read pairs") + args = the_parser.parse_args() + return args + + +if __name__ == "__main__": + args = Parser() + # recover arguments as a dictionary with keys = argument name and values + # are argument values + argsDict = args.__dict__ + ini_lines = [] + # implement first, hard-coded ini lines + ini_lines.append('[manta]') + ini_lines.append('referenceFasta = /dummy/path/to/genome.fa') + # implement the rest of the ini lines for the argsDict + for argument in argsDict: + ini_lines.append("%s = %s" % (argument, str(argsDict[argument]))) + # print ini_lines in configManta.py.ini + handler = open('configManta.py.ini', 'w') + for line in ini_lines: + handler.write("%s\n" % line) diff -r d09254e37c68 -r f55d45b0c6d1 customized.ini --- a/customized.ini Mon Jun 08 03:11:56 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ - -# -# This section contains all configuration settings for the top-level manta workflow, -# -[manta] - -referenceFasta = /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa - -# Run discovery and candidate reporting for all SVs/indels at or above this size -# Separate option (to provide different default) used for runs in RNA-mode -minCandidateVariantSize = 8 -rnaMinCandidateVariantSize = 1000 - -# Remove all edges from the graph unless they're supported by this many 'observations'. -# Note that one supporting read pair or split read usually equals one observation, but evidence is sometimes downweighted. -minEdgeObservations = 3 - -# If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge. -# Set to 0 to turn this filtration off -graphNodeMaxEdgeCount = 10 - -# Run discovery and candidate reporting for all SVs/indels with at least this -# many spanning support observations -minCandidateSpanningCount = 3 - -# After candidate identification, only score and report SVs/indels at or above this size: -minScoredVariantSize = 50 - -# minimum VCF "QUAL" score for a variant to be included in the diploid vcf: -minDiploidVariantScore = 10 - -# VCF "QUAL" score below which a variant is marked as filtered in the diploid vcf: -minPassDiploidVariantScore = 20 - -# minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf: -minPassDiploidGTScore = 15 - -# somatic quality scores below this level are not included in the somatic vcf: -minSomaticScore = 10 - -# somatic quality scores below this level are filtered in the somatic vcf: -minPassSomaticScore = 30 - -# Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote -# locations with poor mapping quality, which pair to confidently mapping reads near the insertion locus. These reads -# can help to fully assemble longer insertions, under certain circumstances this feature can add a very large runtime -# burden. For instance, given the very high chimeric pair rates found in degraded FFPE samples, the runtime of the read -# retrieval process can be unpredicable. For this reason the feature is disabled by default for somatic variant calling. -# This feature can be enabled/disabled separately for germline and cancer calling below. -# -# Here "CancerCallingModes" includes tumor-normal subtraction and tumor-only calling. "GermlineCallingModes" includes -# all other calling modes. -enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1 -enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0 - -# Set if an overlapping read pair will be considered as evidence -# Set to 0 to skip overlapping read pairs -useOverlapPairEvidence = 0 diff -r d09254e37c68 -r f55d45b0c6d1 manta.xml --- a/manta.xml Mon Jun 08 03:11:56 2020 -0400 +++ b/manta.xml Tue Jun 09 06:23:39 2020 -0400 @@ -24,26 +24,27 @@ ln -s '$bam_input.tumor_bam_file.metadata.bam_index' tumor.bai && #end if - #if str( $set_configuration.set_configuration_switch ) == "Customized": - sed -i 's/minCandidateVariantSize = 8/minCandidateVariantSize = $set_configuration.minCandidateVariantSize/' ./configManta.py.ini && - sed -i 's/rnaMinCandidateVariantSize = 1000/rnaMinCandidateVariantSize = $set_configuration.rnaMinCandidateVariantSize/' ./configManta.py.ini && - sed -i 's/minEdgeObservations = 3/minEdgeObservations = $set_configuration.minEdgeObservations/' ./configManta.py.ini && - sed -i 's/graphNodeMaxEdgeCount = 10/graphNodeMaxEdgeCount = $set_configuration.graphNodeMaxEdgeCount/' ./configManta.py.ini && - sed -i 's/minCandidateSpanningCount = 3/minCandidateSpanningCount = $set_configuration.minCandidateSpanningCount/' ./configManta.py.ini && - sed -i 's/minScoredVariantSize = 50/minScoredVariantSize = $set_configuration.minScoredVariantSize/' ./configManta.py.ini && - sed -i 's/minDiploidVariantScore = 10/minDiploidVariantScore = $set_configuration.minDiploidVariantScore/' ./configManta.py.ini && - sed -i 's/minPassDiploidVariantScore = 20/minPassDiploidVariantScore = $set_configuration.minPassDiploidVariantScore/' ./configManta.py.ini && - sed -i 's/minPassDiploidGTScore = 15/minPassDiploidGTScore = $set_configuration.minPassDiploidGTScore/' ./configManta.py.ini && - sed -i 's/minSomaticScore = 10/minSomaticScore = $set_configuration.minSomaticScore/' ./configManta.py.ini && - sed -i 's/minPassSomaticScore = 30/minPassSomaticScore = $set_configuration.minPassSomaticScore/' ./configManta.py.ini && - sed -i 's/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes/' ./configManta.py.ini && - sed -i 's/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes/' ./configManta.py.ini && - sed -i 's/useOverlapPairEvidence = 0/useOverlapPairEvidence = $set_configuration.useOverlapPairEvidence/' ./configManta.py.ini && - #end if - #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file": cp '$set_configuration.CustomConfigFile' ./configManta.py.ini && #end if + #if str( $set_configuration.set_configuration_switch ) == "Customized": + rm ./configManta.py.ini && + python $__tool_directory__/customConfigManta.py + --minCandidateVariantSize '$set_configuration.minCandidateVariantSize' + --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize' + --minEdgeObservations '$set_configuration.minEdgeObservations' + --graphNodeMaxEdgeCount '$set_configuration.graphNodeMaxEdgeCount' + --minCandidateSpanningCount '$set_configuration.minCandidateSpanningCount' + --minScoredVariantSize '$set_configuration.minScoredVariantSize' + --minDiploidVariantScore '$set_configuration.minDiploidVariantScore' + --minPassDiploidVariantScore '$set_configuration.minPassDiploidVariantScore' + --minPassDiploidGTScore '$set_configuration.minPassDiploidGTScore' + --minSomaticScore '$set_configuration.minSomaticScore' + --minPassSomaticScore '$set_configuration.minPassSomaticScore' + --enableRemoteReadRetrievalForInsertionsInGermlineCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes' + --enableRemoteReadRetrievalForInsertionsInCancerCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes' + --useOverlapPairEvidence '$set_configuration.useOverlapPairEvidence' && + #end if configManta.py --referenceFasta='${reference_fasta_filename}' --config='./configManta.py.ini' @@ -53,51 +54,39 @@ --bam='normal.bam' --tumorBam='tumor.bam' #end if - --runDir='${run_dir}' - --scanSizeMb=${advanced.scanSizeMb} - --callMemMb=${advanced.callMemMb} && + --runDir='${run_dir}' + --scanSizeMb=${advanced.scanSizeMb} + --callMemMb=${advanced.callMemMb} && - ln -s -f '${run_dir}/runWorkflow.py' '${run_manta_workflow}' && - ln -s -f './configManta.py.ini' '${set_conf_file}' && python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4} ]]> - - + - - - -
- -
- - - @@ -126,42 +115,32 @@ - - - - - + + - - - - runworkflow_file_check == True - - - + config_file_check == True - + candidateSV_check == True - + candidateSmallIndels_check == True - + diploidSV_check == True - - somaticSV_check == True + + bam_input['bam_input_selector'] == 'tumor_bam' - @@ -172,11 +151,22 @@ - - - + + - + + + + + + + + + + + + + @@ -185,7 +175,8 @@ - + + @@ -196,7 +187,8 @@ - + + @@ -207,10 +199,10 @@ - + + - - + - + ]]> 10.1093/bioinformatics/btv710 - diff -r d09254e37c68 -r f55d45b0c6d1 manta_macros.xml --- a/manta_macros.xml Mon Jun 08 03:11:56 2020 -0400 +++ b/manta_macros.xml Tue Jun 09 06:23:39 2020 -0400 @@ -1,7 +1,7 @@ 1.6 - @VERSION@+galaxy6 + @VERSION@+galaxy7