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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
author artbio
date Tue, 20 Feb 2024 08:31:27 +0000
parents cb5691381acb
children
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7
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
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1 <tool id="manta" name="Manta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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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8
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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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555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
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13 configManta=\$(which configManta.py) &&
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
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14 PATH=\${configManta/"configManta.py"/}:\$PATH &&
555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
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15 printenv &&
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16 cp $__tool_directory__/configManta.py.ini configManta.py.ini &&
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17 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
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18 ln -s '$bam_input.normal_bam_file' normal.bam &&
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19 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai &&
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20 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
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21 ln -s '$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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24 ln -s '$bam_input.tumor_bam_file.metadata.bam_index' tumor.bai &&
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25 #end if
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27 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file":
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28 cp '$set_configuration.CustomConfigFile' ./configManta.py.ini &&
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29 #end if
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30 #if str( $set_configuration.set_configuration_switch ) == "Customized":
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
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31 rm ./configManta.py.ini &&
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555971edd46e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
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32 python2 '$__tool_directory__/customConfigManta.py'
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33 --minCandidateVariantSize '$set_configuration.minCandidateVariantSize'
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34 --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize'
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35 --minEdgeObservations '$set_configuration.minEdgeObservations'
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36 --graphNodeMaxEdgeCount '$set_configuration.graphNodeMaxEdgeCount'
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37 --minCandidateSpanningCount '$set_configuration.minCandidateSpanningCount'
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38 --minScoredVariantSize '$set_configuration.minScoredVariantSize'
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39 --minDiploidVariantScore '$set_configuration.minDiploidVariantScore'
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40 --minPassDiploidVariantScore '$set_configuration.minPassDiploidVariantScore'
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41 --minPassDiploidGTScore '$set_configuration.minPassDiploidGTScore'
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42 --minSomaticScore '$set_configuration.minSomaticScore'
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43 --minPassSomaticScore '$set_configuration.minPassSomaticScore'
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44 --enableRemoteReadRetrievalForInsertionsInGermlineCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes'
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45 --enableRemoteReadRetrievalForInsertionsInCancerCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes'
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46 --useOverlapPairEvidence '$set_configuration.useOverlapPairEvidence' &&
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47 #end if
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48
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49 configManta.py
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50 --referenceFasta='${reference_fasta_filename}'
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51 --config='./configManta.py.ini'
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52 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
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53 --bam='normal.bam'
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54 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
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55 --bam='normal.bam'
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56 --tumorBam='tumor.bam'
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57 #end if
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58 --runDir='${run_dir}'
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59 --scanSizeMb=${advanced.scanSizeMb}
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60 --callMemMb=${advanced.callMemMb} &&
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61
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62 python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4}
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63
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64 ]]></command>
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65 <inputs>
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66 <expand macro="reference_source_conditional" />
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67 <conditional name="bam_input">
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68 <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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69 <option value="not_tumor_bam">Normal</option>
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70 <option value="tumor_bam">Normal + Tumor</option>
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71 </param>
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72 <when value="not_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 </when>
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75 <when value='tumor_bam'>
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76 <param name="normal_bam_file" type="data" format="bam" label="select normal BAM" help="Select the files you wish to send to Manta (normal sample, it must be in BAM format)." />
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77 <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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78 </when>
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79 </conditional>
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80 <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional parameters" >
0
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81 <option value="exome">Set options for WES input: turn off depth filters</option>
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82 <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option>
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83 <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option>
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84 </param>
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85 <section name="advanced" title="Advanced options" expanded="false">
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86 <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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87 <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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88 <!-- <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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89 </section>
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90 <conditional name="set_configuration">
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91 <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?">
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92 <option value="Default_config_file">Default Manta Configuration File</option>
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93 <option value="Custom_config_file">Upload your Own Configuration File</option>
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94 <option value="Customized">Customize a Configuration File using this Galaxy Form</option>
0
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95 </param>
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96 <when value="Default_config_file">
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97 </when>
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98 <when value="Custom_config_file">
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99 <param format="ini" name="CustomConfigFile" type="data" label="config file"/>
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100 </when>
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101 <when value="Customized">
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102 <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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103 <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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104 <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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105 <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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106 <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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107 <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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108 <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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109 <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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110 <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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111 <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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112 <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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113 <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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114 <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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115 <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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116 </when>
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117 </conditional>
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118 <param name="candidateSV_check" type="boolean" label="Unfiltered structural variants" checked="False"
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119 help="All unscored structural variant candidates"/>
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120 <param name="candidateSmallIndels_check" type="boolean" label="Unfiltered small indel candidates" checked="False"
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121 help="Subset of the unscored candidates, containing only small indel variants"/>
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122 <param name="diploidSV_check" type="boolean" label="Score-filtered variants in diploid model" checked="False"
4
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123 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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124 reflect any information from the tumor sample" />
0
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125 </inputs>
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126 <outputs>
7
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127 <data format="txt" name="conf_file" label="conf_file.ini" from_work_dir="./configManta.py.ini"/>
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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>
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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>
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142 <test expect_num_outputs="3">
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="conf_file" file="conf_file_1.ini" ftype="txt"/>
6
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152 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
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153 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
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154 </test>
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155 <test expect_num_outputs="3">
6
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156 <param name="reference_source_selector" value="cached"/>
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157 <param name="index" value="hg19"/>
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158 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
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159 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
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160 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
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161 <param name="set_configuration_switch" value="Customized"/>
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162 <param name="callMemMb" value="1000"/>
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163 <param name="candidateSmallIndels_check" value="True"/>
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164 <output name="conf_file" file="conf_file_2.ini" ftype="txt"/>
6
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165 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
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166 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
5
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167 </test>
7
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168 <test expect_num_outputs="3">
4
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169 <param name="reference_source_selector" value="cached"/>
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170 <param name="index" value="hg19"/>
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171 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
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172 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
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173 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
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174 <param name="set_configuration_switch" value="Default_config_file"/>
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175 <param name="callMemMb" value="1000"/>
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176 <param name="candidateSmallIndels_check" value="True"/>
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177 <output name="conf_file" file="conf_file_3.ini" ftype="txt"/>
5
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178 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
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179 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
4
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180 </test>
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181 <test expect_num_outputs="3">
4
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182 <param name="reference_source_selector" value="history"/>
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183 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
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184 <param name="bam_input_selector" value="tumor_bam"/>
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185 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
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186 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
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187 <param name="set_configuration_switch" value="Default_config_file"/>
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188 <param name="callMemMb" value="1000"/>
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189 <param name="candidateSV_check" value="True"/>
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190 <output name="conf_file" file="conf_file_4.ini" ftype="txt"/>
5
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191 <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="6"/>
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192 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
4
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193 </test>
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194 <test expect_num_outputs="3">
4
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195 <param name="reference_source_selector" value="history"/>
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196 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
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197 <param name="bam_input_selector" value="tumor_bam"/>
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198 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
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199 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
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200 <param name="set_configuration_switch" value="Default_config_file"/>
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201 <param name="callMemMb" value="1000"/>
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202 <param name="candidateSmallIndels_check" value="True"/>
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203 <output name="conf_file" file="conf_file_5.ini" ftype="txt"/>
5
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204 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
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205 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
4
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206 </test>
5
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207 </tests>
4
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208 <help><![CDATA[
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209 **Outputs**
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210 The primary Manta outputs are a set of VCF 4.1 files. Currently there are 3 VCF files
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211 created for a germline analysis, and an additional somatic VCF is produced for a
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212 tumor/normal subtraction. These files are:
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213
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214 - diploidSV.vcf.gz
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215 SVs and indels scored and genotyped under a diploid model for the set of samples in a
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216 joint diploid sample analysis or for the normal sample in a tumor/normal subtraction
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217 analysis. **In the case of a tumor/normal subtraction, the scores in this file do not
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218 reflect any information from the tumor sample.**
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219
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220 - somaticSV.vcf.gz
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221 SVs and indels scored under a somatic variant model. This file will only be produced
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222 if a tumor sample alignment file is supplied during configuration
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223
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224 - candidateSV.vcf.gz
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225 Unscored SV and indel candidates. Only a minimal amount of supporting evidence is
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226 required for an SV to be entered as a candidate in this file. An SV or indel must be a
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227 candidate to be considered for scoring, therefore an SV cannot appear in the other VCF
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228 outputs if it is not present in this file. Note that by default this file includes
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229 indels of size 8 and larger. The smallest indels in this set are intended to be passed
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230 on to a small variant caller without scoring by manta itself (by default manta scoring
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231 starts at size 50).
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232
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233 - candidateSmallIndels.vcf.gz
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234 Subset of the candidateSV.vcf.gz file containing only simple insertion and deletion
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235 variants less than the minimum scored variant size (50 by default). Passing this file
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236 to a small variant caller will provide continuous coverage over all indel sizes when
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237 the small variant caller and manta outputs are evaluated together. Alternate small
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238 indel candidate sets can be parsed out of the candidateSV.vcf.gz file if this
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239 candidate set is not appropriate.
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240
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241 For tumor-only analysis, Manta will produce an additional VCF:
0
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242
4
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243 - tumorSV.vcf.gz
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244 Subset of the candidateSV.vcf.gz file after removing redundant candidates and small
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245 indels less than the minimum scored variant size (50 by default). The SVs are not
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246 scored, but include additional details: (1) paired and split read supporting evidence
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247 counts for each allele (2) a subset of the filters from the scored tumor-normal model
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248 are applied to the single tumor case to improve precision.
0
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249
4
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250 **Manta helps**
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251 This script configures the Manta SV analysis pipeline.
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252 You must specify a BAM or CRAM file for at least one sample.
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253 Configuration will produce a workflow run script which
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254 can execute the workflow on a single node or through
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255 sge and resume any interrupted execution.
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256
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257
6
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258 For further info see: https://github.com/Illumina/manta
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259
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260 ]]></help>
0
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261 <citations>
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262 <citation type="doi">10.1093/bioinformatics/btv710</citation>
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263 </citations>
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264 </tool>