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annotate manta.xml @ 3:d648e40c6da9 draft

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"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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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'
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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16 cp $__tool_directory__/configManta.py.ini configManta.py.ini &&
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17 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
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d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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18 ln -s '$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 '$bam_input.normal_bam_file.metadata.bam_index' normal.bai &&
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23 ln -s '$bam_input.tumor_bam_file' tumor.bam &&
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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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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 &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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33 sed -i 's/minScoredVariantSize = 50/minScoredVariantSize = $set_configuration.minScoredVariantSize/' ./configManta.py.ini &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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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 &&
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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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 &&
0
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42 #end if
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43
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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47
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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48 configManta.py --referenceFasta='${reference_fasta_filename}'
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
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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' '${set_conf_file}' &&
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62 python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4} &&
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63 cp '${run_dir}/results/variants/candidateSV.vcf.gz' '${out_vcf1}' &&
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64 cp '${run_dir}/results/variants/diploidSV.vcf.gz' '${out_vcf2}' &&
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65 cp '${run_dir}/results/variants/candidateSmallIndels.vcf.gz' '${out_vcf3}'
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66
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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67 ]]></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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69 <inputs>
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70 <expand macro="reference_source_conditional" />
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71
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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72 <conditional name="bam_input">
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73 <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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74 <option value="not_tumor_bam">Normal</option>
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75 <option value="tumor_bam">Normal + Tumor</option>
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76 </param>
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77
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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78 <when value="not_tumor_bam">
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79 <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)." />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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80 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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81
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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82 <when value='tumor_bam'>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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83 <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)." />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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84 <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)." />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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85 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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86 </conditional>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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87
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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88 <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional outputs" help="Additional parameters.">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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89 <option value="exome">Set options for WES input: turn off depth filters</option>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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90 <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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91 <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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92 </param>
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93
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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94 <section name="advanced" title="Advanced options" expanded="false">
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95
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96 <param name="callMemMb" type="integer" value="8000" label="Set default task memory requirements" help="The maximum memory size to assign to tasks" />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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97 <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)" />
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98 <param name="retainTempFiles" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Keep all temporary files" help="Click yes so all temporary files (for workflow debugging) will be kept."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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99 <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."/>
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100
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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101 </section>
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102
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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103 <!-- <expand macro="manta_configuration"/> -->
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104
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105 <conditional name="set_configuration">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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106 <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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107 <option value="Default_config_file">Default</option>
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108 <option value="Custom_config_file">Upload a different config file</option>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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109 <option value="Customized">Customize the options</option>
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110 </param>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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111 <when value="Default_config_file">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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112 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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113 <when value="Custom_config_file">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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114 <param format="ini" name="CustomConfigFile" type="data" label="config file"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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115 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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116 <when value="Customized">
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117 <param name="minCandidateVariantSize" type="integer" value="8" label="minCandidateVariantSize" help="Run discovery and candidate reporting for all SVs/indels at or above this size."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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118 <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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119 <param name="minEdgeObservations" type="integer" value="3" label="minEdgeObservations" help="Remove all edges from the graph unless they're supported by this many 'observations'."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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120 <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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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121 <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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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122 <param name="minScoredVariantSize" type="integer" value="50" label="minScoredVariantSize" help="After candidate identification, only score and report SVs/indels at or above this size."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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123 <param name="minDiploidVariantScore" type="integer" value="10" label="minDiploidVariantScore" help="Minimum VCF 'QUAL' score for a variant to be included in the diploid vcf."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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124 <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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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125 <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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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126 <param name="minSomaticScore" type="integer" value="10" label="minSomaticScore" help="Somatic quality scores below this level are not included in the somatic vcf."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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127 <param name="minPassSomaticScore" type="integer" value="30" label="minPassSomaticScore" help="Somatic quality scores below this level are filtered in the somatic vcf."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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128 <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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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129 <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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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130 <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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131 </when>
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132 </conditional>
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133
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134 <param name="runworkflow_file_check" type="boolean" label="output manta run_workflow file" checked="False" help="Show run_workflow file on history"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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135 <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/>
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136 <param name="O1_check" type="boolean" label="snvs filtred" checked="False" help="Show filtred snvs"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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137 <param name="O2_check" type="boolean" label="indels filtred" checked="False" help="Show filtred indels"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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138 <param name="O3_check" type="boolean" label="all snvs" checked="False" help="Show snvs"/>
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139
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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140 </inputs>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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141
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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142 <outputs>
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143
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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144 <data format="txt" name="run_manta_workflow" label="Parameters for running Manta">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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145 <filter>runworkflow_file_check == True</filter>
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146 </data>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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147
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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148 <data format="tabular" name="set_conf_file" label="conf_file.ini">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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149 <filter>config_file_check == True</filter>
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150 </data>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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151 <data format="vcf_bgzip" name="out_vcf1" label="${tool.name} on ${on_string} (Generating the candidateSV.vcf file)" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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152 <filter>O1_check == True</filter>
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153 </data>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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154 <data format="vcf_bgzip" name="out_vcf2" label="${tool.name} on ${on_string} (Generating the diploidSV.vcf file)" from_work_dir="MantaWorkflow/results/variants/diploidSV.vcf.gz">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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155 <filter>O2_check == True</filter>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
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156 </data>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
157 <data format="vcf_bgzip" name="out_vcf3" label="${tool.name} on ${on_string} (Generating the candidateSmallIndels.vcf file)" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
158 <filter>O3_check == True</filter>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
159 </data>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
160 </outputs>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
161
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
162 <tests>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
163 <test>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
164 <conditional name="reference_source">
3
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
165 <param name="reference_source_selector" value="cached"/>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
166 <param name="index" value="hg19"/>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
167 </conditional>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
168
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
169 <conditional name="bam_input">
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
170 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
171 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
172 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
173 </conditional>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
174
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
175 <conditional name="set_configuration">
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
176 <param name="set_configuration_switch" value="Default_config_file"/>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
177 </conditional>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
178 <param name="callMemMb" value="1000"/>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
179 <param name="O3_check" value="True"/>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
180 <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
181 </test>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
182 <test>
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
183 <conditional name="reference_source">
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
184 <param name="reference_source_selector" value="history"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
185 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
186 </conditional>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
187
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
188 <conditional name="bam_input">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
189 <param name="bam_input_selector" value="tumor_bam"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
190 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
191 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
192 </conditional>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
193
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
194 <conditional name="set_configuration">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
195 <param name="set_configuration_switch" value="Default_config_file"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
196 </conditional>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
197 <param name="callMemMb" value="1000"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
198 <param name="O1_check" value="True"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
199 <output name="out_vcf1" file="candidateSV.vcf.gz" decompress="true" lines_diff="4"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
200 </test>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
201 <test>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
202 <conditional name="reference_source">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
203 <param name="reference_source_selector" value="history"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
204 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
205 </conditional>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
206
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
207 <conditional name="bam_input">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
208 <param name="bam_input_selector" value="tumor_bam"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
209 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
210 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
211 </conditional>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
212
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
213 <conditional name="set_configuration">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
214 <param name="set_configuration_switch" value="Default_config_file"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
215 </conditional>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
216 <param name="callMemMb" value="1000"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
217 <param name="O3_check" value="True"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
218 <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
219 </test>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
220 </tests>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
221
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
222 <help><![CDATA[
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
223 **Manta**
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
224 This script configures the Manta SV analysis pipeline.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
225 You must specify a BAM or CRAM file for at least one sample.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
226 Configuration will produce a workflow run script which
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
227 can execute the workflow on a single node or through
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
228 sge and resume any interrupted execution.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
229
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
230 **Options**
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
231 --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
parents:
diff changeset
232 -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"
artbio
parents:
diff changeset
233 --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
parents:
diff changeset
234 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
parents:
diff changeset
235 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"
artbio
parents:
diff changeset
236 --allHelp show all extended/hidden options
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
237 **Workflow options**
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
238 --bam=FILE, --normalBam=FILE
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
239 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
parents:
diff changeset
240 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
parents:
diff changeset
241 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
parents:
diff changeset
242 default)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
243 --tumorBam=FILE, --tumourBam=FILE
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
244 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"
artbio
parents:
diff changeset
245 bam file accepted. [optional] (no default)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
246 --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
parents:
diff changeset
247 --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
parents:
diff changeset
248 one bam input file
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
249 --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
parents:
diff changeset
250 junctions on either strand
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
251 --referenceFasta=FILE
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
252 samtools-indexed reference fasta file [required]
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
253 --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
parents:
diff changeset
254 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
parents:
diff changeset
255 requires a separate directory. (default:
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
256 MantaWorkflow)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
257 --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"
artbio
parents:
diff changeset
258 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"
artbio
parents:
diff changeset
259 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"
artbio
parents:
diff changeset
260 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"
artbio
parents:
diff changeset
261 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"
artbio
parents:
diff changeset
262 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"
artbio
parents:
diff changeset
263 (default: call the entire genome)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
264 **Extended options**
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
265 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"
artbio
parents:
diff changeset
266 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"
artbio
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diff changeset
267 They will not be printed here if a default exists unless --allHelp is
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
268 specified
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
269 --existingAlignStatsFile=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
270 Pre-calculated alignment statistics file. Skips
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
271 alignment stats calculation.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
272 --useExistingChromDepths
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
273 Use pre-calculated chromosome depths.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
274 --candidateBins=candidateBins
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
275 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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diff changeset
276 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
parents:
diff changeset
277 --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"
artbio
parents:
diff changeset
278 --generateEvidenceBam
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
279 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"
artbio
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diff changeset
280 --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"
artbio
parents:
diff changeset
281 --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
parents:
diff changeset
282 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"
artbio
parents:
diff changeset
283 12)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
284 --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
parents:
diff changeset
285 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
parents:
diff changeset
286 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
parents:
diff changeset
287 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"
artbio
parents:
diff changeset
288 meaningful result. Examples: '--region chr20' (whole
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
289 chromosome), '--region chr2:100-2000 --region
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
290 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
parents:
diff changeset
291 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
parents:
diff changeset
292 --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
parents:
diff changeset
293 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
parents:
diff changeset
294 --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
parents:
diff changeset
295 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
parents:
diff changeset
296 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
parents:
diff changeset
297 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
parents:
diff changeset
298 creation and candidate generation.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
299
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
300 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"
artbio
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diff changeset
301
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
302 ]]></help>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
303
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
304 <citations>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
305 <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"
artbio
parents:
diff changeset
306 </citations>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
307
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
308 </tool>