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annotate manta.xml @ 4:d09254e37c68 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
author artbio
date Mon, 08 Jun 2020 03:11:56 -0400
parents d648e40c6da9
children f55d45b0c6d1
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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1 <tool id="manta" name="Manta" version="@WRAPPER_VERSION@">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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3 <description>Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.</description>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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5 <macros>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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6 <import>manta_macros.xml</import>
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7 </macros>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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11 <command detect_errors="exit_code"><![CDATA[
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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12 @VERSION@
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13 @pipefail@
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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14 @set_reference_fasta_filename@
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15 #set run_dir = './MantaWorkflow'
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16 cp $__tool_directory__/configManta.py.ini configManta.py.ini &&
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17 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
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18 ln -s '$bam_input.normal_bam_file' normal.bam &&
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19 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai &&
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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20 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
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d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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21 ln -s '$bam_input.normal_bam_file' normal.bam &&
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22 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai &&
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d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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23 ln -s '$bam_input.tumor_bam_file' tumor.bam &&
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24 ln -s '$bam_input.tumor_bam_file.metadata.bam_index' tumor.bai &&
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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25 #end if
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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27 #if str( $set_configuration.set_configuration_switch ) == "Customized":
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28 sed -i 's/minCandidateVariantSize = 8/minCandidateVariantSize = $set_configuration.minCandidateVariantSize/' ./configManta.py.ini &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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29 sed -i 's/rnaMinCandidateVariantSize = 1000/rnaMinCandidateVariantSize = $set_configuration.rnaMinCandidateVariantSize/' ./configManta.py.ini &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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30 sed -i 's/minEdgeObservations = 3/minEdgeObservations = $set_configuration.minEdgeObservations/' ./configManta.py.ini &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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31 sed -i 's/graphNodeMaxEdgeCount = 10/graphNodeMaxEdgeCount = $set_configuration.graphNodeMaxEdgeCount/' ./configManta.py.ini &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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32 sed -i 's/minCandidateSpanningCount = 3/minCandidateSpanningCount = $set_configuration.minCandidateSpanningCount/' ./configManta.py.ini &&
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33 sed -i 's/minScoredVariantSize = 50/minScoredVariantSize = $set_configuration.minScoredVariantSize/' ./configManta.py.ini &&
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34 sed -i 's/minDiploidVariantScore = 10/minDiploidVariantScore = $set_configuration.minDiploidVariantScore/' ./configManta.py.ini &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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35 sed -i 's/minPassDiploidVariantScore = 20/minPassDiploidVariantScore = $set_configuration.minPassDiploidVariantScore/' ./configManta.py.ini &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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36 sed -i 's/minPassDiploidGTScore = 15/minPassDiploidGTScore = $set_configuration.minPassDiploidGTScore/' ./configManta.py.ini &&
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37 sed -i 's/minSomaticScore = 10/minSomaticScore = $set_configuration.minSomaticScore/' ./configManta.py.ini &&
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38 sed -i 's/minPassSomaticScore = 30/minPassSomaticScore = $set_configuration.minPassSomaticScore/' ./configManta.py.ini &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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39 sed -i 's/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes/' ./configManta.py.ini &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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40 sed -i 's/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes/' ./configManta.py.ini &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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41 sed -i 's/useOverlapPairEvidence = 0/useOverlapPairEvidence = $set_configuration.useOverlapPairEvidence/' ./configManta.py.ini &&
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42 #end if
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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44 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file":
3
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45 cp '$set_configuration.CustomConfigFile' ./configManta.py.ini &&
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46 #end if
3
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48 configManta.py --referenceFasta='${reference_fasta_filename}'
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49 --config='./configManta.py.ini'
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50 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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51 --bam='normal.bam'
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52 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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53 --bam='normal.bam'
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54 --tumorBam='tumor.bam'
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55 #end if
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56 --runDir='${run_dir}'
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57 --scanSizeMb=${advanced.scanSizeMb}
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58 --callMemMb=${advanced.callMemMb} &&
0
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59
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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60 ln -s -f '${run_dir}/runWorkflow.py' '${run_manta_workflow}' &&
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61 ln -s -f './configManta.py.ini' '${set_conf_file}' &&
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d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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62 python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4}
0
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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64 ]]></command>
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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66 <inputs>
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67 <expand macro="reference_source_conditional" />
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68
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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69 <conditional name="bam_input">
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70 <param name="bam_input_selector" type="select" label="Just 'normal' BAM file or 'normal' + 'tumor' BAM files" help="Select between a single normal BAM file or a pair of normal / tumor BAM files">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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71 <option value="not_tumor_bam">Normal</option>
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72 <option value="tumor_bam">Normal + Tumor</option>
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73 </param>
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74
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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75 <when value="not_tumor_bam">
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76 <param name="normal_bam_file" type="data" format="bam" label="select normal BAM" help="Select the files you wish to send to Manta (normal sample, it must be in BAM format)." />
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77 </when>
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42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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79 <when value='tumor_bam'>
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80 <param name="normal_bam_file" type="data" format="bam" label="select normal BAM" help="Select the files you wish to send to Manta (normal sample, it must be in BAM format)." />
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81 <param name="tumor_bam_file" type="data" format="bam" label="select tumor BAM" help="Select the files you wish to send to Manta (tumor sample, it must be in BAM format)." />
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82 </when>
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83 </conditional>
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84
4
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85 <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional parameters" >
0
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86 <option value="exome">Set options for WES input: turn off depth filters</option>
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87 <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option>
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88 <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option>
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89 </param>
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90
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91 <section name="advanced" title="Advanced options" expanded="false">
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92
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93 <param name="callMemMb" type="integer" value="8000" label="Set default task memory requirements" help="The maximum memory size to assign to tasks" />
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94 <param name="scanSizeMb" type="integer" value="12" label="Set maximum sequence region size" help="The maximum sequence region size (in megabases) scanned by each task during SV Locus graph generation. (default: 12)" />
4
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95 <!-- <param name="generateEvidenceBam" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Generate a bam of supporting reads for all SVs" help="Click yes for generating a BAM of supporting reads for all SVs."/> -->
0
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96
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97 </section>
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98
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99 <!-- <expand macro="manta_configuration"/> -->
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100
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101 <conditional name="set_configuration">
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102 <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?">
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103 <option value="Default_config_file">Default Manta Configuration File</option>
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104 <option value="Custom_config_file">Upload your Own Configuration File</option>
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105 <option value="Customized">Customize a Configuration File using this Galaxy Form</option>
0
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106 </param>
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107 <when value="Default_config_file">
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108 </when>
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109 <when value="Custom_config_file">
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110 <param format="ini" name="CustomConfigFile" type="data" label="config file"/>
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111 </when>
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112 <when value="Customized">
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113 <param name="minCandidateVariantSize" type="integer" value="8" label="minCandidateVariantSize" help="Run discovery and candidate reporting for all SVs/indels at or above this size."/>
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114 <param name="rnaMinCandidateVariantSize" type="integer" value="1000" label="rnaMinCandidateVariantSize" help="Separate option (to provide different default) used for runs in RNA-mode."/>
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115 <param name="minEdgeObservations" type="integer" value="3" label="minEdgeObservations" help="Remove all edges from the graph unless they're supported by this many 'observations'."/>
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116 <param name="graphNodeMaxEdgeCount" type="integer" value="10" label="graphNodeMaxEdgeCount" help="If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge."/>
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117 <param name="minCandidateSpanningCount" type="integer" value="3" label="minCandidateSpanningCount" help="Run discovery and candidate reporting for all SVs/indels with at least this many spanning support observations."/>
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118 <param name="minScoredVariantSize" type="integer" value="50" label="minScoredVariantSize" help="After candidate identification, only score and report SVs/indels at or above this size."/>
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119 <param name="minDiploidVariantScore" type="integer" value="10" label="minDiploidVariantScore" help="Minimum VCF 'QUAL' score for a variant to be included in the diploid vcf."/>
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120 <param name="minPassDiploidVariantScore" type="integer" value="20" label="minPassDiploidVariantScore" help="VCF 'QUAL' score below which a variant is marked as filtered in the diploid vcf."/>
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121 <param name="minPassDiploidGTScore" type="integer" value="15" label="minPassDiploidGTScore" help="Minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf."/>
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122 <param name="minSomaticScore" type="integer" value="10" label="minSomaticScore" help="Somatic quality scores below this level are not included in the somatic vcf."/>
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123 <param name="minPassSomaticScore" type="integer" value="30" label="minPassSomaticScore" help="Somatic quality scores below this level are filtered in the somatic vcf."/>
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124 <param name="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" type="integer" value="1" label="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" help="Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote locations with poor mapping quality. This feature can be enabled/disabled separately for germline and cancer calling below."/>
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125 <param name="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" type="integer" value="0" label="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" help="Here 'CancerCallingModes' includes tumor-normal subtraction and tumor-only calling. 'GermlineCallingModes' includes all other calling modes."/>
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126 <param name="useOverlapPairEvidence" type="integer" value="0" label="useOverlapPairEvidence" help="Set if an overlapping read pair will be considered as evidence. Set this value &lt;= 0 to skip overlapping read pairs."/>
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127 </when>
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128 </conditional>
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129
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130 <param name="runworkflow_file_check" type="boolean" label="output manta run_workflow file" checked="False" help="Show run_workflow file on history"/>
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131 <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/>
4
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132 <param name="candidateSV_check" type="boolean" label="Unscored candidate SV and indels" checked="False"
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133 help="Show unfiltered structural variants"/>
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134 <param name="candidateSmallIndels_check" type="boolean" label="all snvs" checked="False"
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135 help="Subset of the Unscored candidate SV and indels, containing only simple insertion and deletion variants"/>
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136 <param name="diploidSV_check" type="boolean" label="filtered variants in diploid model" checked="False"
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137 help="Show filtered variants in a diploid (only normal) model. In the case of a tumor/normal subtraction, the scores in this file *do not*
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138 reflect any information from the tumor sample" />
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139 <param name="somaticSV_check" type="boolean" label="SVs and indels scored under a somatic variant model" checked="False"
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140 help="This file will only be produced if a tumor sample alignment file is supplied during configuration"/>
0
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141 </inputs>
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142
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143 <outputs>
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144 <data format="txt" name="run_manta_workflow" label="Parameters for running Manta">
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145 <filter>runworkflow_file_check == True</filter>
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146 </data>
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147
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148 <data format="tabular" name="set_conf_file" label="conf_file.ini">
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149 <filter>config_file_check == True</filter>
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150 </data>
4
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151 <data format="vcf_bgzip" name="candidateSV" label="Manta unfiltered SVs" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz">
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152 <filter>candidateSV_check == True</filter>
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153 </data>
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154 <data format="vcf_bgzip" name="candidateSmallIndels" label="Manta unfiltered Small Indels" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz">
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155 <filter>candidateSmallIndels_check == True</filter>
0
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156 </data>
4
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157 <data format="vcf_bgzip" name="diploidSV" label="Manta SVs (diploid model)" from_work_dir="MantaWorkflow/results/variants/diploidSV.vcf.gz">
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158 <filter>diploidSV_check == True</filter>
0
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159 </data>
4
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160 <data format="vcf_bgzip" name="somaticSV" label="Manta SVs (somatic model)" from_work_dir="MantaWorkflow/results/variants/somaticSV.vcf.gz">
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161 <filter>somaticSV_check == True</filter>
0
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162 </data>
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163 </outputs>
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164
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165 <tests>
4
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166 <test>
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167 <param name="reference_source_selector" value="cached"/>
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168 <param name="index" value="hg19"/>
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169 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
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170 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
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171 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
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172 <param name="set_configuration_switch" value="Default_config_file"/>
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173 <param name="callMemMb" value="1000"/>
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174 <param name="candidateSmallIndels_check" value="True"/>
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175 <param name="somaticSV_check" value="True"/>
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176 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
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177 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="4"/>
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178 </test>
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179 <test>
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180 <param name="reference_source_selector" value="cached"/>
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181 <param name="index" value="hg19"/>
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182 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
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183 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
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184 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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185 <param name="set_configuration_switch" value="Default_config_file"/>
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186 <param name="callMemMb" value="1000"/>
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187 <param name="candidateSmallIndels_check" value="True"/>
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188 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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189 </test>
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190 <test>
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191 <param name="reference_source_selector" value="history"/>
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192 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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193 <param name="bam_input_selector" value="tumor_bam"/>
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194 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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195 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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196 <param name="set_configuration_switch" value="Default_config_file"/>
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197 <param name="callMemMb" value="1000"/>
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198 <param name="candidateSV_check" value="True"/>
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199 <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="4"/>
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200 </test>
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201 <test>
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202 <param name="reference_source_selector" value="history"/>
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203 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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204 <param name="bam_input_selector" value="tumor_bam"/>
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artbio
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205 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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206 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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207 <param name="set_configuration_switch" value="Default_config_file"/>
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208 <param name="callMemMb" value="1000"/>
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209 <param name="candidateSmallIndels_check" value="True"/>
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210 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
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211 </test>
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212 </tests>
0
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213
4
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214 <help><![CDATA[
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215 **Outputs**
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216 The primary Manta outputs are a set of VCF 4.1 files. Currently there are 3 VCF files
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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217 created for a germline analysis, and an additional somatic VCF is produced for a
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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218 tumor/normal subtraction. These files are:
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219
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220 - diploidSV.vcf.gz
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221 SVs and indels scored and genotyped under a diploid model for the set of samples in a
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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222 joint diploid sample analysis or for the normal sample in a tumor/normal subtraction
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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223 analysis. **In the case of a tumor/normal subtraction, the scores in this file do not
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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224 reflect any information from the tumor sample.**
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225
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226 - somaticSV.vcf.gz
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227 SVs and indels scored under a somatic variant model. This file will only be produced
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228 if a tumor sample alignment file is supplied during configuration
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229
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230 - candidateSV.vcf.gz
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231 Unscored SV and indel candidates. Only a minimal amount of supporting evidence is
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232 required for an SV to be entered as a candidate in this file. An SV or indel must be a
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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233 candidate to be considered for scoring, therefore an SV cannot appear in the other VCF
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234 outputs if it is not present in this file. Note that by default this file includes
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235 indels of size 8 and larger. The smallest indels in this set are intended to be passed
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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236 on to a small variant caller without scoring by manta itself (by default manta scoring
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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237 starts at size 50).
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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238
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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239 - candidateSmallIndels.vcf.gz
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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240 Subset of the candidateSV.vcf.gz file containing only simple insertion and deletion
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241 variants less than the minimum scored variant size (50 by default). Passing this file
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242 to a small variant caller will provide continuous coverage over all indel sizes when
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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243 the small variant caller and manta outputs are evaluated together. Alternate small
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artbio
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244 indel candidate sets can be parsed out of the candidateSV.vcf.gz file if this
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diff changeset
245 candidate set is not appropriate.
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246
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artbio
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247 For tumor-only analysis, Manta will produce an additional VCF:
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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248
4
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artbio
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249 - tumorSV.vcf.gz
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
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250 Subset of the candidateSV.vcf.gz file after removing redundant candidates and small
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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251 indels less than the minimum scored variant size (50 by default). The SVs are not
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
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252 scored, but include additional details: (1) paired and split read supporting evidence
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
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diff changeset
253 counts for each allele (2) a subset of the filters from the scored tumor-normal model
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
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diff changeset
254 are applied to the single tumor case to improve precision.
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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255
4
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artbio
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256 **Manta helps**
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artbio
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257 This script configures the Manta SV analysis pipeline.
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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258 You must specify a BAM or CRAM file for at least one sample.
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
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259 Configuration will produce a workflow run script which
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
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260 can execute the workflow on a single node or through
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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261 sge and resume any interrupted execution.
0
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262
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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263 **Options**
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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264 --version show program's version number and exit
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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265 -h, --help show this help message and exit
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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266 --config=FILE provide a configuration file to override defaults in
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
267 global config file (/home/lpanunzi/Desktop/Hackaton_GC
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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268 C2019/manta_sv/manta/bin/configManta.py.ini)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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269 --allHelp show all extended/hidden options
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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270 **Workflow options**
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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diff changeset
271 --bam=FILE, --normalBam=FILE
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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272 Normal sample BAM or CRAM file. May be specified more
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
273 than once, multiple inputs will be treated as each BAM
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
274 file representing a different sample. [optional] (no
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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275 default)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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276 --tumorBam=FILE, --tumourBam=FILE
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
277 Tumor sample BAM or CRAM file. Only up to one tumor
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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diff changeset
278 bam file accepted. [optional] (no default)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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279 --exome Set options for WES input: turn off depth filters
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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280 --rna Set options for RNA-Seq input. Must specify exactly
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
281 one bam input file
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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282 --unstrandedRNA Set if RNA-Seq input is unstranded: Allows splice-
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
283 junctions on either strand
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
284 --referenceFasta=FILE
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
285 samtools-indexed reference fasta file [required]
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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286 --runDir=DIR Name of directory to be created where all workflow
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
287 scripts and output will be written. Each analysis
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
288 requires a separate directory. (default:
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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289 MantaWorkflow)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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290 --callRegions=FILE Optionally provide a bgzip-compressed/tabix-indexed
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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291 BED file containing the set of regions to call. No VCF
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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292 output will be provided outside of these regions. The
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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293 full genome will still be used to estimate statistics
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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294 from the input (such as expected fragment size
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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295 distribution). Only one BED file may be specified.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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296 (default: call the entire genome)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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297 **Extended options**
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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298 These options are either unlikely to be reset after initial site
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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diff changeset
299 configuration or only of interest for workflow development/debugging.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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300 They will not be printed here if a default exists unless --allHelp is
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artbio
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301 specified
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
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diff changeset
302
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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diff changeset
303 --existingAlignStatsFile=FILE
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304 Pre-calculated alignment statistics file. Skips
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
305 alignment stats calculation.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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306 --useExistingChromDepths
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
307 Use pre-calculated chromosome depths.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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308 --candidateBins=candidateBins
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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309 Provide the total number of tasks which candidate
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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310 generation will be sub-divided into. (default: 256)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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311 --retainTempFiles Keep all temporary files (for workflow debugging)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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312 --generateEvidenceBam
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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313 Generate a bam of supporting reads for all SVs
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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314 --outputContig Output assembled contig sequences in VCF file
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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315 --scanSizeMb=INT Maximum sequence region size (in megabases) scanned by
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
316 each task during SV Locus graph generation. (default:
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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317 12)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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318 --region=REGION Limit the analysis to a region of the genome for
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
319 debugging purposes. If this argument is provided
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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320 multiple times all specified regions will be analyzed
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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321 together. All regions must be non-overlapping to get a
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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322 meaningful result. Examples: '--region chr20' (whole
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
323 chromosome), '--region chr2:100-2000 --region
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
324 chr3:2500-3000' (two regions)'. If this option is
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
325 specified (one or more times) together with the
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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326 --callRegions BED file, then all region arguments will
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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327 be intersected with the callRegions BED track.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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328 --callMemMb=INT Set default task memory requirement (in megabytes) for
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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329 common tasks. This may benefit an analysis of unusual
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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diff changeset
330 depth, chimera rate, etc.. 'Common' tasks refers to
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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331 most compute intensive scatter-phase tasks of graph
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
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332 creation and candidate generation.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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333
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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334 For further info see: https://github.com/Illumina/manta
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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335
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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336 ]]></help>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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337
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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338 <citations>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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339 <citation type="doi">10.1093/bioinformatics/btv710</citation>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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340 </citations>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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341
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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342 </tool>