| Previous changeset 2:6a69e5d7c21f (2020-06-07) Next changeset 4:d09254e37c68 (2020-06-08) |
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Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b" |
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modified:
manta.xml manta_macros.xml |
| b |
| diff -r 6a69e5d7c21f -r d648e40c6da9 manta.xml --- a/manta.xml Sun Jun 07 09:08:06 2020 -0400 +++ b/manta.xml Sun Jun 07 16:43:54 2020 -0400 |
| [ |
| b'@@ -12,73 +12,57 @@\n @VERSION@\n @pipefail@\n @set_reference_fasta_filename@\n-\n- #import os\n- #import random\n- #set job_dir=os.getcwd()\n- #set run_dir = job_dir + \'/MantaWorkflow_\' + (\' \' + str(random.randint(1,100000))).strip()\n- #set config_file = $__tool_directory__ + \'/configManta.py.ini\'\n- #set config_file_custom = $__tool_directory__ + \'/customized.ini\' \n- #set $input_normal = \'normal.bam\'\n- #set $input_tumor = \'tumor.bam\'\n-\n+ #set run_dir = \'./MantaWorkflow\'\n+ cp $__tool_directory__/configManta.py.ini configManta.py.ini &&\n #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":\n- ln -s \'$bam_input.normal_bam_file\' $input_normal &&\n+ ln -s \'$bam_input.normal_bam_file\' normal.bam &&\n ln -s \'$bam_input.normal_bam_file.metadata.bam_index\' normal.bai &&\n #else if str( $bam_input.bam_input_selector ) == "tumor_bam":\n- ln -s \'$bam_input.normal_bam_file\' $input_normal &&\n+ ln -s \'$bam_input.normal_bam_file\' normal.bam &&\n ln -s \'$bam_input.normal_bam_file.metadata.bam_index\' normal.bai &&\n- ln -s \'$bam_input.tumor_bam_file\' $input_tumor &&\n+ ln -s \'$bam_input.tumor_bam_file\' tumor.bam &&\n ln -s \'$bam_input.tumor_bam_file.metadata.bam_index\' tumor.bai &&\n #end if\n \n- cp ${config_file} ${config_file_custom} &&\n-\n #if str( $set_configuration.set_configuration_switch ) == "Customized":\n- sed -i \'s/minCandidateVariantSize = 8/minCandidateVariantSize = $set_configuration.minCandidateVariantSize/\' ${config_file_custom} &&\n- sed -i \'s/rnaMinCandidateVariantSize = 1000/rnaMinCandidateVariantSize = $set_configuration.rnaMinCandidateVariantSize/\' ${config_file_custom} &&\n- sed -i \'s/minEdgeObservations = 3/minEdgeObservations = $set_configuration.minEdgeObservations/\' ${config_file_custom} &&\n- sed -i \'s/graphNodeMaxEdgeCount = 10/graphNodeMaxEdgeCount = $set_configuration.graphNodeMaxEdgeCount/\' ${config_file_custom} &&\n- sed -i \'s/minCandidateSpanningCount = 3/minCandidateSpanningCount = $set_configuration.minCandidateSpanningCount/\' ${config_file_custom} &&\n- sed -i \'s/minScoredVariantSize = 50/minScoredVariantSize = $set_configuration.minScoredVariantSize/\' ${config_file_custom} &&\n- sed -i \'s/minDiploidVariantScore = 10/minDiploidVariantScore = $set_configuration.minDiploidVariantScore/\' ${config_file_custom} &&\n- sed -i \'s/minPassDiploidVariantScore = 20/minPassDiploidVariantScore = $set_configuration.minPassDiploidVariantScore/\' ${config_file_custom} &&\n- sed -i \'s/minPassDiploidGTScore = 15/minPassDiploidGTScore = $set_configuration.minPassDiploidGTScore/\' ${config_file_custom} &&\n- sed -i \'s/minSomaticScore = 10/minSomaticScore = $set_configuration.minSomaticScore/\' ${config_file_custom} &&\n- sed -i \'s/minPassSomaticScore = 30/minPassSomaticScore = $set_configuration.minPassSomaticScore/\' ${config_file_custom} &&\n- sed -i \'s/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes/\' ${config_file_custom} &&\n- sed -i \'s/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes/\' ${config_file_custom} &&\n- sed -i \'s/useOverlapPairEvidence = 0/useOverlapPairEvidence = $set_configuration.useOverlapPairEvidence/\' ${config_file_custom} &&\n+ sed -i \'s/minCandidateVariantSize = 8/minCandidateVariantSize = $set_configuration.minCandidateVariantSize/\' ./configManta.py.ini &&\n+ sed -i \'s/rnaMinCandidateVariantSize = 1000/rnaMinCandidateVariantSize = $set_configuration.rnaMinCandidateVariantSize/\' ./configManta.py.ini &&\n+ sed -i \'s/minEdgeObservations = 3/minEdgeObservations = $set_configuration.minEdgeObservations/\' ./configManta.py.ini &&\n+ sed -i \'s/graphNodeMaxEdgeCount = 10/graphNo'..b'am\'\n+ --tumorBam=\'tumor.bam\'\n+ #end if\n+ --runDir=\'${run_dir}\'\n+ --scanSizeMb=${advanced.scanSizeMb}\n+ --callMemMb=${advanced.callMemMb} &&\n \n ln -s -f \'${run_dir}/runWorkflow.py\' \'${run_manta_workflow}\' &&\n- ln -s -f \'${config_file}\' \'${set_conf_file}\' &&\n- python2 \'${run_dir}/runWorkflow.py\' -m local -j 8 &&\n- ln -s -f \'${run_dir}/results/variants/candidateSV.vcf.gz\' \'${out_vcf1}\' &&\n- ln -s -f \'${run_dir}/results/variants/diploidSV.vcf.gz\' \'${out_vcf2}\' &&\n- ln -s -f \'${run_dir}/results/variants/candidateSmallIndels.vcf.gz\' \'${out_vcf3}\'\n+ ln -s -f \'./configManta.py.ini\' \'${set_conf_file}\' &&\n+ python2 \'${run_dir}/runWorkflow.py\' -m local -j \\${GALAXY_SLOTS:-4} &&\n+ cp \'${run_dir}/results/variants/candidateSV.vcf.gz\' \'${out_vcf1}\' &&\n+ cp \'${run_dir}/results/variants/diploidSV.vcf.gz\' \'${out_vcf2}\' &&\n+ cp \'${run_dir}/results/variants/candidateSmallIndels.vcf.gz\' \'${out_vcf3}\'\n \n ]]></command>\n \n@@ -178,6 +162,25 @@\n <tests>\n <test>\n <conditional name="reference_source">\n+ <param name="reference_source_selector" value="cached"/>\n+ <param name="index" value="hg19"/>\n+ </conditional>\n+\n+ <conditional name="bam_input">\n+ <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>\n+ <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>\n+ <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>\n+ </conditional>\n+\n+ <conditional name="set_configuration">\n+ <param name="set_configuration_switch" value="Default_config_file"/>\n+ </conditional>\n+ <param name="callMemMb" value="1000"/>\n+ <param name="O3_check" value="True"/>\n+ <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>\n+ </test>\n+ <test>\n+ <conditional name="reference_source">\n <param name="reference_source_selector" value="history"/>\n <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>\n </conditional>\n@@ -214,25 +217,6 @@\n <param name="O3_check" value="True"/>\n <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>\n </test>\n- <test>\n- <conditional name="reference_source">\n- <param name="reference_source_selector" value="cached"/>\n- <param name="index" value="hg19"/>\n- </conditional>\n-\n- <conditional name="bam_input">\n- <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>\n- <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>\n- <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>\n- </conditional>\n-\n- <conditional name="set_configuration">\n- <param name="set_configuration_switch" value="Default_config_file"/>\n- </conditional>\n- <param name="callMemMb" value="1000"/>\n- <param name="O3_check" value="True"/>\n- <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>\n- </test>\n </tests>\n \n <help><![CDATA[\n' |
| b |
| diff -r 6a69e5d7c21f -r d648e40c6da9 manta_macros.xml --- a/manta_macros.xml Sun Jun 07 09:08:06 2020 -0400 +++ b/manta_macros.xml Sun Jun 07 16:43:54 2020 -0400 |
| [ |
| @@ -1,14 +1,14 @@ <macros> <token name="@VERSION@">1.6</token> - <token name="@WRAPPER_VERSION@">@VERSION@+galaxy4</token> + <token name="@WRAPPER_VERSION@">@VERSION@+galaxy5</token> <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> <token name="@set_reference_fasta_filename@"><![CDATA[ #set $reference_fasta_filename = "localref.fa" #if str( $reference_source.reference_source_selector ) == "history": - ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' && + ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 && #else: #set $reference_fasta_filename = str( $reference_source.index.fields.path ) @@ -21,7 +21,7 @@ #else if str( $configuration.configuration_switch )== "Customized": #set $config_file = '$configuration.Customized' #else: - #set $config_file = $__tool_directory__ + '/configManta.py.ini' + #set $config_file = 'configManta.py.ini' #end if ]]></token> |