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annotate manta.xml @ 6:cb5691381acb draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 01bc6749826f5ef4a22540a9aa6a5ffd93786d4c
author artbio
date Thu, 08 Jun 2023 17:36:38 +0000
parents f55d45b0c6d1
children 555971edd46e
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cb5691381acb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 01bc6749826f5ef4a22540a9aa6a5ffd93786d4c
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1 <tool id="manta" name="Manta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.</description>
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3 <macros>
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4 <import>manta_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @pipefail@
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11 @set_reference_fasta_filename@
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12 #set run_dir = './MantaWorkflow'
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13 cp $__tool_directory__/configManta.py.ini configManta.py.ini &&
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14 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
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15 ln -s '$bam_input.normal_bam_file' normal.bam &&
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16 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai &&
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17 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
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18 ln -s '$bam_input.normal_bam_file' normal.bam &&
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19 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai &&
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20 ln -s '$bam_input.tumor_bam_file' tumor.bam &&
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21 ln -s '$bam_input.tumor_bam_file.metadata.bam_index' tumor.bai &&
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22 #end if
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23
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24 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file":
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25 cp '$set_configuration.CustomConfigFile' ./configManta.py.ini &&
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26 #end if
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27 #if str( $set_configuration.set_configuration_switch ) == "Customized":
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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28 rm ./configManta.py.ini &&
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cb5691381acb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 01bc6749826f5ef4a22540a9aa6a5ffd93786d4c
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29 python '$__tool_directory__/customConfigManta.py'
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30 --minCandidateVariantSize '$set_configuration.minCandidateVariantSize'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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31 --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize'
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32 --minEdgeObservations '$set_configuration.minEdgeObservations'
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33 --graphNodeMaxEdgeCount '$set_configuration.graphNodeMaxEdgeCount'
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34 --minCandidateSpanningCount '$set_configuration.minCandidateSpanningCount'
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35 --minScoredVariantSize '$set_configuration.minScoredVariantSize'
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36 --minDiploidVariantScore '$set_configuration.minDiploidVariantScore'
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37 --minPassDiploidVariantScore '$set_configuration.minPassDiploidVariantScore'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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38 --minPassDiploidGTScore '$set_configuration.minPassDiploidGTScore'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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39 --minSomaticScore '$set_configuration.minSomaticScore'
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40 --minPassSomaticScore '$set_configuration.minPassSomaticScore'
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41 --enableRemoteReadRetrievalForInsertionsInGermlineCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes'
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42 --enableRemoteReadRetrievalForInsertionsInCancerCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes'
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43 --useOverlapPairEvidence '$set_configuration.useOverlapPairEvidence' &&
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44 #end if
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45
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46 configManta.py
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47 --referenceFasta='${reference_fasta_filename}'
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48 --config='./configManta.py.ini'
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49 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
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50 --bam='normal.bam'
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51 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
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52 --bam='normal.bam'
cb5691381acb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 01bc6749826f5ef4a22540a9aa6a5ffd93786d4c
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53 --tumorBam='tumor.bam'
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54 #end if
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55 --runDir='${run_dir}'
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56 --scanSizeMb=${advanced.scanSizeMb}
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57 --callMemMb=${advanced.callMemMb} &&
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58
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59 python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4}
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60
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61 ]]></command>
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62 <inputs>
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63 <expand macro="reference_source_conditional" />
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64 <conditional name="bam_input">
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65 <param name="bam_input_selector" type="select" label="Single 'normal' or 'normal vs tumor' analysis" help="Select between a single normal BAM file or a pair of normal/tumor BAM files">
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66 <option value="not_tumor_bam">Normal</option>
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67 <option value="tumor_bam">Normal + Tumor</option>
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68 </param>
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69 <when value="not_tumor_bam">
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70 <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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71 </when>
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72 <when value='tumor_bam'>
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73 <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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74 <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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75 </when>
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76 </conditional>
4
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77 <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional parameters" >
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78 <option value="exome">Set options for WES input: turn off depth filters</option>
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79 <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option>
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80 <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option>
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81 </param>
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82 <section name="advanced" title="Advanced options" expanded="false">
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83 <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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84 <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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85 <!-- <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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86 </section>
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87 <conditional name="set_configuration">
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88 <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?">
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89 <option value="Default_config_file">Default Manta Configuration File</option>
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90 <option value="Custom_config_file">Upload your Own Configuration File</option>
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91 <option value="Customized">Customize a Configuration File using this Galaxy Form</option>
0
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92 </param>
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93 <when value="Default_config_file">
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94 </when>
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95 <when value="Custom_config_file">
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96 <param format="ini" name="CustomConfigFile" type="data" label="config file"/>
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97 </when>
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98 <when value="Customized">
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99 <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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100 <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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101 <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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102 <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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103 <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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104 <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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105 <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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106 <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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107 <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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108 <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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109 <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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110 <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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111 <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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112 <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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113 </when>
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114 </conditional>
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115 <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/>
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116 <param name="candidateSV_check" type="boolean" label="Unfiltered structural variants" checked="False"
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117 help="All unscored structural variant candidates"/>
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118 <param name="candidateSmallIndels_check" type="boolean" label="Unfiltered small indel candidates" checked="False"
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119 help="Subset of the unscored candidates, containing only small indel variants"/>
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120 <param name="diploidSV_check" type="boolean" label="Score-filtered variants in diploid model" checked="False"
4
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121 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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122 reflect any information from the tumor sample" />
0
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123 </inputs>
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124 <outputs>
5
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125 <data format="tabular" name="conf_file" label="conf_file.ini" from_work_dir="./configManta.py.ini">
0
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126 <filter>config_file_check == True</filter>
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127 </data>
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128 <data format="vcf_bgzip" name="candidateSV" label="Manta unfiltered variants" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz">
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129 <filter>candidateSV_check == True</filter>
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130 </data>
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131 <data format="vcf_bgzip" name="candidateSmallIndels" label="Manta unfiltered indels" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz">
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132 <filter>candidateSmallIndels_check == True</filter>
0
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133 </data>
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134 <data format="vcf_bgzip" name="diploidSV" label="Score-filtered Variants (diploid model)" from_work_dir="MantaWorkflow/results/variants/diploidSV.vcf.gz">
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135 <filter>diploidSV_check == True</filter>
0
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136 </data>
5
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137 <data format="vcf_bgzip" name="somaticSV" label="Score-filtered Variants (somatic model)" from_work_dir="MantaWorkflow/results/variants/somaticSV.vcf.gz">
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138 <filter>bam_input['bam_input_selector'] == 'tumor_bam'</filter>
0
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139 </data>
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140 </outputs>
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141 <tests>
4
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142 <test>
6
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143 <param name="reference_source_selector" value="cached"/>
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144 <param name="index" value="hg19"/>
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145 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
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146 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
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147 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
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148 <param name="set_configuration_switch" value="Default_config_file"/>
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149 <param name="callMemMb" value="1000"/>
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150 <param name="candidateSmallIndels_check" value="True"/>
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151 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
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152 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
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153 </test>
6
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154 <test>
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155 <param name="reference_source_selector" value="cached"/>
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156 <param name="index" value="hg19"/>
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157 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
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158 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
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159 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
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160 <param name="set_configuration_switch" value="Customized"/>
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161 <param name="callMemMb" value="1000"/>
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162 <param name="candidateSmallIndels_check" value="True"/>
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163 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
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164 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
5
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165 </test>
6
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166 <test>
4
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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 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
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176 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
4
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177 </test>
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178 <test>
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179 <param name="reference_source_selector" value="history"/>
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180 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
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181 <param name="bam_input_selector" value="tumor_bam"/>
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182 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
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183 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
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184 <param name="set_configuration_switch" value="Default_config_file"/>
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185 <param name="callMemMb" value="1000"/>
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186 <param name="candidateSV_check" value="True"/>
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187 <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="6"/>
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188 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
4
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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"/>
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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"/>
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195 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
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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="candidateSmallIndels_check" value="True"/>
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199 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
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200 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
4
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201 </test>
5
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202 </tests>
4
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203 <help><![CDATA[
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204 **Outputs**
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205 The primary Manta outputs are a set of VCF 4.1 files. Currently there are 3 VCF files
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206 created for a germline analysis, and an additional somatic VCF is produced for a
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207 tumor/normal subtraction. These files are:
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208
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209 - diploidSV.vcf.gz
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210 SVs and indels scored and genotyped under a diploid model for the set of samples in a
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211 joint diploid sample analysis or for the normal sample in a tumor/normal subtraction
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212 analysis. **In the case of a tumor/normal subtraction, the scores in this file do not
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213 reflect any information from the tumor sample.**
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214
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215 - somaticSV.vcf.gz
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216 SVs and indels scored under a somatic variant model. This file will only be produced
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217 if a tumor sample alignment file is supplied during configuration
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218
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219 - candidateSV.vcf.gz
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220 Unscored SV and indel candidates. Only a minimal amount of supporting evidence is
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221 required for an SV to be entered as a candidate in this file. An SV or indel must be a
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222 candidate to be considered for scoring, therefore an SV cannot appear in the other VCF
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223 outputs if it is not present in this file. Note that by default this file includes
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224 indels of size 8 and larger. The smallest indels in this set are intended to be passed
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225 on to a small variant caller without scoring by manta itself (by default manta scoring
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226 starts at size 50).
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227
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228 - candidateSmallIndels.vcf.gz
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229 Subset of the candidateSV.vcf.gz file containing only simple insertion and deletion
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230 variants less than the minimum scored variant size (50 by default). Passing this file
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231 to a small variant caller will provide continuous coverage over all indel sizes when
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232 the small variant caller and manta outputs are evaluated together. Alternate small
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233 indel candidate sets can be parsed out of the candidateSV.vcf.gz file if this
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234 candidate set is not appropriate.
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235
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236 For tumor-only analysis, Manta will produce an additional VCF:
0
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237
4
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238 - tumorSV.vcf.gz
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
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239 Subset of the candidateSV.vcf.gz file after removing redundant candidates and small
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240 indels less than the minimum scored variant size (50 by default). The SVs are not
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241 scored, but include additional details: (1) paired and split read supporting evidence
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242 counts for each allele (2) a subset of the filters from the scored tumor-normal model
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243 are applied to the single tumor case to improve precision.
0
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244
4
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245 **Manta helps**
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246 This script configures the Manta SV analysis pipeline.
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247 You must specify a BAM or CRAM file for at least one sample.
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248 Configuration will produce a workflow run script which
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249 can execute the workflow on a single node or through
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250 sge and resume any interrupted execution.
0
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251
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252
6
cb5691381acb planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 01bc6749826f5ef4a22540a9aa6a5ffd93786d4c
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253 For further info see: https://github.com/Illumina/manta
0
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254
5
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255 ]]></help>
0
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256 <citations>
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257 <citation type="doi">10.1093/bioinformatics/btv710</citation>
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258 </citations>
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259 </tool>