Mercurial > repos > artbio > manta
diff manta.xml @ 3:d648e40c6da9 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
| author | artbio |
|---|---|
| date | Sun, 07 Jun 2020 16:43:54 -0400 |
| parents | 42ba283a0fe2 |
| children | d09254e37c68 |
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--- a/manta.xml Sun Jun 07 09:08:06 2020 -0400 +++ b/manta.xml Sun Jun 07 16:43:54 2020 -0400 @@ -12,73 +12,57 @@ @VERSION@ @pipefail@ @set_reference_fasta_filename@ - - #import os - #import random - #set job_dir=os.getcwd() - #set run_dir = job_dir + '/MantaWorkflow_' + (' ' + str(random.randint(1,100000))).strip() - #set config_file = $__tool_directory__ + '/configManta.py.ini' - #set config_file_custom = $__tool_directory__ + '/customized.ini' - #set $input_normal = 'normal.bam' - #set $input_tumor = 'tumor.bam' - + #set run_dir = './MantaWorkflow' + cp $__tool_directory__/configManta.py.ini configManta.py.ini && #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": - ln -s '$bam_input.normal_bam_file' $input_normal && + ln -s '$bam_input.normal_bam_file' normal.bam && ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai && #else if str( $bam_input.bam_input_selector ) == "tumor_bam": - ln -s '$bam_input.normal_bam_file' $input_normal && + ln -s '$bam_input.normal_bam_file' normal.bam && ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai && - ln -s '$bam_input.tumor_bam_file' $input_tumor && + ln -s '$bam_input.tumor_bam_file' tumor.bam && ln -s '$bam_input.tumor_bam_file.metadata.bam_index' tumor.bai && #end if - cp ${config_file} ${config_file_custom} && - #if str( $set_configuration.set_configuration_switch ) == "Customized": - sed -i 's/minCandidateVariantSize = 8/minCandidateVariantSize = $set_configuration.minCandidateVariantSize/' ${config_file_custom} && - sed -i 's/rnaMinCandidateVariantSize = 1000/rnaMinCandidateVariantSize = $set_configuration.rnaMinCandidateVariantSize/' ${config_file_custom} && - sed -i 's/minEdgeObservations = 3/minEdgeObservations = $set_configuration.minEdgeObservations/' ${config_file_custom} && - sed -i 's/graphNodeMaxEdgeCount = 10/graphNodeMaxEdgeCount = $set_configuration.graphNodeMaxEdgeCount/' ${config_file_custom} && - sed -i 's/minCandidateSpanningCount = 3/minCandidateSpanningCount = $set_configuration.minCandidateSpanningCount/' ${config_file_custom} && - sed -i 's/minScoredVariantSize = 50/minScoredVariantSize = $set_configuration.minScoredVariantSize/' ${config_file_custom} && - sed -i 's/minDiploidVariantScore = 10/minDiploidVariantScore = $set_configuration.minDiploidVariantScore/' ${config_file_custom} && - sed -i 's/minPassDiploidVariantScore = 20/minPassDiploidVariantScore = $set_configuration.minPassDiploidVariantScore/' ${config_file_custom} && - sed -i 's/minPassDiploidGTScore = 15/minPassDiploidGTScore = $set_configuration.minPassDiploidGTScore/' ${config_file_custom} && - sed -i 's/minSomaticScore = 10/minSomaticScore = $set_configuration.minSomaticScore/' ${config_file_custom} && - sed -i 's/minPassSomaticScore = 30/minPassSomaticScore = $set_configuration.minPassSomaticScore/' ${config_file_custom} && - sed -i 's/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes/' ${config_file_custom} && - sed -i 's/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes/' ${config_file_custom} && - sed -i 's/useOverlapPairEvidence = 0/useOverlapPairEvidence = $set_configuration.useOverlapPairEvidence/' ${config_file_custom} && + 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 = $set_configuration.useOverlapPairEvidence/' ./configManta.py.ini && #end if - configManta.py - --referenceFasta='${reference_fasta_filename}' - #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file": - #set config_file = $set_configuration.CustomConfigFile - #else if str( $set_configuration.set_configuration_switch ) == "Customized": - #set config_file = config_file_custom + cp '$set_configuration.CustomConfigFile' ./configManta.py.ini && #end if - - --config=${config_file} - - #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": - --bam=$input_normal - #else if str( $bam_input.bam_input_selector ) == "tumor_bam": - --bam=$input_normal - --tumorBam=$input_tumor - #end if - - --runDir='${run_dir}' - --scanSizeMb=${advanced.scanSizeMb} - --callMemMb=${advanced.callMemMb} && + + configManta.py --referenceFasta='${reference_fasta_filename}' + --config='./configManta.py.ini' + #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": + --bam='normal.bam' + #else if str( $bam_input.bam_input_selector ) == "tumor_bam": + --bam='normal.bam' + --tumorBam='tumor.bam' + #end if + --runDir='${run_dir}' + --scanSizeMb=${advanced.scanSizeMb} + --callMemMb=${advanced.callMemMb} && ln -s -f '${run_dir}/runWorkflow.py' '${run_manta_workflow}' && - ln -s -f '${config_file}' '${set_conf_file}' && - python2 '${run_dir}/runWorkflow.py' -m local -j 8 && - ln -s -f '${run_dir}/results/variants/candidateSV.vcf.gz' '${out_vcf1}' && - ln -s -f '${run_dir}/results/variants/diploidSV.vcf.gz' '${out_vcf2}' && - ln -s -f '${run_dir}/results/variants/candidateSmallIndels.vcf.gz' '${out_vcf3}' + ln -s -f './configManta.py.ini' '${set_conf_file}' && + python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4} && + cp '${run_dir}/results/variants/candidateSV.vcf.gz' '${out_vcf1}' && + cp '${run_dir}/results/variants/diploidSV.vcf.gz' '${out_vcf2}' && + cp '${run_dir}/results/variants/candidateSmallIndels.vcf.gz' '${out_vcf3}' ]]></command> @@ -178,6 +162,25 @@ <tests> <test> <conditional name="reference_source"> + <param name="reference_source_selector" value="cached"/> + <param name="index" value="hg19"/> + </conditional> + + <conditional name="bam_input"> + <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> + <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> + <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> + </conditional> + + <conditional name="set_configuration"> + <param name="set_configuration_switch" value="Default_config_file"/> + </conditional> + <param name="callMemMb" value="1000"/> + <param name="O3_check" value="True"/> + <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/> + </test> + <test> + <conditional name="reference_source"> <param name="reference_source_selector" value="history"/> <param name="ref_file" ftype="fasta" value="hg19_region.fa"/> </conditional> @@ -214,25 +217,6 @@ <param name="O3_check" value="True"/> <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/> </test> - <test> - <conditional name="reference_source"> - <param name="reference_source_selector" value="cached"/> - <param name="index" value="hg19"/> - </conditional> - - <conditional name="bam_input"> - <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> - <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> - <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> - </conditional> - - <conditional name="set_configuration"> - <param name="set_configuration_switch" value="Default_config_file"/> - </conditional> - <param name="callMemMb" value="1000"/> - <param name="O3_check" value="True"/> - <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/> - </test> </tests> <help><![CDATA[