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comparison manta.xml @ 5:f55d45b0c6d1 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
author artbio
date Tue, 09 Jun 2020 06:23:39 -0400
parents d09254e37c68
children cb5691381acb
comparison
equal deleted inserted replaced
4:d09254e37c68 5:f55d45b0c6d1
22 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai && 22 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai &&
23 ln -s '$bam_input.tumor_bam_file' tumor.bam && 23 ln -s '$bam_input.tumor_bam_file' tumor.bam &&
24 ln -s '$bam_input.tumor_bam_file.metadata.bam_index' tumor.bai && 24 ln -s '$bam_input.tumor_bam_file.metadata.bam_index' tumor.bai &&
25 #end if 25 #end if
26 26
27 #if str( $set_configuration.set_configuration_switch ) == "Customized":
28 sed -i 's/minCandidateVariantSize = 8/minCandidateVariantSize = $set_configuration.minCandidateVariantSize/' ./configManta.py.ini &&
29 sed -i 's/rnaMinCandidateVariantSize = 1000/rnaMinCandidateVariantSize = $set_configuration.rnaMinCandidateVariantSize/' ./configManta.py.ini &&
30 sed -i 's/minEdgeObservations = 3/minEdgeObservations = $set_configuration.minEdgeObservations/' ./configManta.py.ini &&
31 sed -i 's/graphNodeMaxEdgeCount = 10/graphNodeMaxEdgeCount = $set_configuration.graphNodeMaxEdgeCount/' ./configManta.py.ini &&
32 sed -i 's/minCandidateSpanningCount = 3/minCandidateSpanningCount = $set_configuration.minCandidateSpanningCount/' ./configManta.py.ini &&
33 sed -i 's/minScoredVariantSize = 50/minScoredVariantSize = $set_configuration.minScoredVariantSize/' ./configManta.py.ini &&
34 sed -i 's/minDiploidVariantScore = 10/minDiploidVariantScore = $set_configuration.minDiploidVariantScore/' ./configManta.py.ini &&
35 sed -i 's/minPassDiploidVariantScore = 20/minPassDiploidVariantScore = $set_configuration.minPassDiploidVariantScore/' ./configManta.py.ini &&
36 sed -i 's/minPassDiploidGTScore = 15/minPassDiploidGTScore = $set_configuration.minPassDiploidGTScore/' ./configManta.py.ini &&
37 sed -i 's/minSomaticScore = 10/minSomaticScore = $set_configuration.minSomaticScore/' ./configManta.py.ini &&
38 sed -i 's/minPassSomaticScore = 30/minPassSomaticScore = $set_configuration.minPassSomaticScore/' ./configManta.py.ini &&
39 sed -i 's/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes/' ./configManta.py.ini &&
40 sed -i 's/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes/' ./configManta.py.ini &&
41 sed -i 's/useOverlapPairEvidence = 0/useOverlapPairEvidence = $set_configuration.useOverlapPairEvidence/' ./configManta.py.ini &&
42 #end if
43
44 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file": 27 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file":
45 cp '$set_configuration.CustomConfigFile' ./configManta.py.ini && 28 cp '$set_configuration.CustomConfigFile' ./configManta.py.ini &&
29 #end if
30 #if str( $set_configuration.set_configuration_switch ) == "Customized":
31 rm ./configManta.py.ini &&
32 python $__tool_directory__/customConfigManta.py
33 --minCandidateVariantSize '$set_configuration.minCandidateVariantSize'
34 --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize'
35 --minEdgeObservations '$set_configuration.minEdgeObservations'
36 --graphNodeMaxEdgeCount '$set_configuration.graphNodeMaxEdgeCount'
37 --minCandidateSpanningCount '$set_configuration.minCandidateSpanningCount'
38 --minScoredVariantSize '$set_configuration.minScoredVariantSize'
39 --minDiploidVariantScore '$set_configuration.minDiploidVariantScore'
40 --minPassDiploidVariantScore '$set_configuration.minPassDiploidVariantScore'
41 --minPassDiploidGTScore '$set_configuration.minPassDiploidGTScore'
42 --minSomaticScore '$set_configuration.minSomaticScore'
43 --minPassSomaticScore '$set_configuration.minPassSomaticScore'
44 --enableRemoteReadRetrievalForInsertionsInGermlineCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes'
45 --enableRemoteReadRetrievalForInsertionsInCancerCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes'
46 --useOverlapPairEvidence '$set_configuration.useOverlapPairEvidence' &&
46 #end if 47 #end if
47 48
48 configManta.py --referenceFasta='${reference_fasta_filename}' 49 configManta.py --referenceFasta='${reference_fasta_filename}'
49 --config='./configManta.py.ini' 50 --config='./configManta.py.ini'
50 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": 51 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
51 --bam='normal.bam' 52 --bam='normal.bam'
52 #else if str( $bam_input.bam_input_selector ) == "tumor_bam": 53 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
53 --bam='normal.bam' 54 --bam='normal.bam'
54 --tumorBam='tumor.bam' 55 --tumorBam='tumor.bam'
55 #end if 56 #end if
56 --runDir='${run_dir}' 57 --runDir='${run_dir}'
57 --scanSizeMb=${advanced.scanSizeMb} 58 --scanSizeMb=${advanced.scanSizeMb}
58 --callMemMb=${advanced.callMemMb} && 59 --callMemMb=${advanced.callMemMb} &&
59 60
60 ln -s -f '${run_dir}/runWorkflow.py' '${run_manta_workflow}' &&
61 ln -s -f './configManta.py.ini' '${set_conf_file}' &&
62 python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4} 61 python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4}
63 62
64 ]]></command> 63 ]]></command>
65 64
66 <inputs> 65 <inputs>
67 <expand macro="reference_source_conditional" /> 66 <expand macro="reference_source_conditional" />
68
69 <conditional name="bam_input"> 67 <conditional name="bam_input">
70 <param name="bam_input_selector" type="select" label="Just 'normal' BAM file or 'normal' + 'tumor' BAM files" help="Select between a single normal BAM file or a pair of normal / tumor BAM files"> 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">
71 <option value="not_tumor_bam">Normal</option> 69 <option value="not_tumor_bam">Normal</option>
72 <option value="tumor_bam">Normal + Tumor</option> 70 <option value="tumor_bam">Normal + Tumor</option>
73 </param> 71 </param>
74
75 <when value="not_tumor_bam"> 72 <when value="not_tumor_bam">
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)." /> 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)." />
77 </when> 74 </when>
78
79 <when value='tumor_bam'> 75 <when value='tumor_bam'>
80 <param name="normal_bam_file" type="data" format="bam" label="select normal BAM" help="Select the files you wish to send to Manta (normal sample, it must be in BAM format)." /> 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)." />
81 <param name="tumor_bam_file" type="data" format="bam" label="select tumor BAM" help="Select the files you wish to send to Manta (tumor sample, it must be in BAM format)." /> 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)." />
82 </when> 78 </when>
83 </conditional> 79 </conditional>
84
85 <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional parameters" > 80 <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional parameters" >
86 <option value="exome">Set options for WES input: turn off depth filters</option> 81 <option value="exome">Set options for WES input: turn off depth filters</option>
87 <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option> 82 <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option>
88 <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option> 83 <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option>
89 </param> 84 </param>
90
91 <section name="advanced" title="Advanced options" expanded="false"> 85 <section name="advanced" title="Advanced options" expanded="false">
92
93 <param name="callMemMb" type="integer" value="8000" label="Set default task memory requirements" help="The maximum memory size to assign to tasks" /> 86 <param name="callMemMb" type="integer" value="8000" label="Set default task memory requirements" help="The maximum memory size to assign to tasks" />
94 <param name="scanSizeMb" type="integer" value="12" label="Set maximum sequence region size" help="The maximum sequence region size (in megabases) scanned by each task during SV Locus graph generation. (default: 12)" /> 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)" />
95 <!-- <param name="generateEvidenceBam" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Generate a bam of supporting reads for all SVs" help="Click yes for generating a BAM of supporting reads for all SVs."/> --> 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."/> -->
96
97 </section> 89 </section>
98
99 <!-- <expand macro="manta_configuration"/> -->
100
101 <conditional name="set_configuration"> 90 <conditional name="set_configuration">
102 <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?"> 91 <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?">
103 <option value="Default_config_file">Default Manta Configuration File</option> 92 <option value="Default_config_file">Default Manta Configuration File</option>
104 <option value="Custom_config_file">Upload your Own Configuration File</option> 93 <option value="Custom_config_file">Upload your Own Configuration File</option>
105 <option value="Customized">Customize a Configuration File using this Galaxy Form</option> 94 <option value="Customized">Customize a Configuration File using this Galaxy Form</option>
124 <param name="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" type="integer" value="1" label="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" help="Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote locations with poor mapping quality. This feature can be enabled/disabled separately for germline and cancer calling below."/> 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."/>
125 <param name="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" type="integer" value="0" label="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" help="Here 'CancerCallingModes' includes tumor-normal subtraction and tumor-only calling. 'GermlineCallingModes' includes all other calling modes."/> 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."/>
126 <param name="useOverlapPairEvidence" type="integer" value="0" label="useOverlapPairEvidence" help="Set if an overlapping read pair will be considered as evidence. Set this value &lt;= 0 to skip overlapping read pairs."/> 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."/>
127 </when> 116 </when>
128 </conditional> 117 </conditional>
129
130 <param name="runworkflow_file_check" type="boolean" label="output manta run_workflow file" checked="False" help="Show run_workflow file on history"/>
131 <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/> 118 <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/>
132 <param name="candidateSV_check" type="boolean" label="Unscored candidate SV and indels" checked="False" 119 <param name="candidateSV_check" type="boolean" label="Unfiltered structural variants" checked="False"
133 help="Show unfiltered structural variants"/> 120 help="All unscored structural variant candidates"/>
134 <param name="candidateSmallIndels_check" type="boolean" label="all snvs" checked="False" 121 <param name="candidateSmallIndels_check" type="boolean" label="Unfiltered small indel candidates" checked="False"
135 help="Subset of the Unscored candidate SV and indels, containing only simple insertion and deletion variants"/> 122 help="Subset of the unscored candidates, containing only small indel variants"/>
136 <param name="diploidSV_check" type="boolean" label="filtered variants in diploid model" checked="False" 123 <param name="diploidSV_check" type="boolean" label="Score-filtered variants in diploid model" checked="False"
137 help="Show filtered variants in a diploid (only normal) model. In the case of a tumor/normal subtraction, the scores in this file *do not* 124 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*
138 reflect any information from the tumor sample" /> 125 reflect any information from the tumor sample" />
139 <param name="somaticSV_check" type="boolean" label="SVs and indels scored under a somatic variant model" checked="False"
140 help="This file will only be produced if a tumor sample alignment file is supplied during configuration"/>
141 </inputs> 126 </inputs>
142
143 <outputs> 127 <outputs>
144 <data format="txt" name="run_manta_workflow" label="Parameters for running Manta"> 128 <data format="tabular" name="conf_file" label="conf_file.ini" from_work_dir="./configManta.py.ini">
145 <filter>runworkflow_file_check == True</filter>
146 </data>
147
148 <data format="tabular" name="set_conf_file" label="conf_file.ini">
149 <filter>config_file_check == True</filter> 129 <filter>config_file_check == True</filter>
150 </data> 130 </data>
151 <data format="vcf_bgzip" name="candidateSV" label="Manta unfiltered SVs" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz"> 131 <data format="vcf_bgzip" name="candidateSV" label="Manta unfiltered variants" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz">
152 <filter>candidateSV_check == True</filter> 132 <filter>candidateSV_check == True</filter>
153 </data> 133 </data>
154 <data format="vcf_bgzip" name="candidateSmallIndels" label="Manta unfiltered Small Indels" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz"> 134 <data format="vcf_bgzip" name="candidateSmallIndels" label="Manta unfiltered indels" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz">
155 <filter>candidateSmallIndels_check == True</filter> 135 <filter>candidateSmallIndels_check == True</filter>
156 </data> 136 </data>
157 <data format="vcf_bgzip" name="diploidSV" label="Manta SVs (diploid model)" from_work_dir="MantaWorkflow/results/variants/diploidSV.vcf.gz"> 137 <data format="vcf_bgzip" name="diploidSV" label="Score-filtered Variants (diploid model)" from_work_dir="MantaWorkflow/results/variants/diploidSV.vcf.gz">
158 <filter>diploidSV_check == True</filter> 138 <filter>diploidSV_check == True</filter>
159 </data> 139 </data>
160 <data format="vcf_bgzip" name="somaticSV" label="Manta SVs (somatic model)" from_work_dir="MantaWorkflow/results/variants/somaticSV.vcf.gz"> 140 <data format="vcf_bgzip" name="somaticSV" label="Score-filtered Variants (somatic model)" from_work_dir="MantaWorkflow/results/variants/somaticSV.vcf.gz">
161 <filter>somaticSV_check == True</filter> 141 <filter>bam_input['bam_input_selector'] == 'tumor_bam'</filter>
162 </data> 142 </data>
163 </outputs> 143 </outputs>
164
165 <tests> 144 <tests>
166 <test> 145 <test>
167 <param name="reference_source_selector" value="cached"/> 146 <param name="reference_source_selector" value="cached"/>
168 <param name="index" value="hg19"/> 147 <param name="index" value="hg19"/>
169 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> 148 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
170 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 149 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
171 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 150 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
172 <param name="set_configuration_switch" value="Default_config_file"/> 151 <param name="set_configuration_switch" value="Default_config_file"/>
173 <param name="callMemMb" value="1000"/> 152 <param name="callMemMb" value="1000"/>
174 <param name="candidateSmallIndels_check" value="True"/> 153 <param name="candidateSmallIndels_check" value="True"/>
175 <param name="somaticSV_check" value="True"/> 154 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
176 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/> 155 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
177 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="4"/> 156 </test>
178 </test> 157 <test>
179 <test>
180 <param name="reference_source_selector" value="cached"/> 158 <param name="reference_source_selector" value="cached"/>
181 <param name="index" value="hg19"/> 159 <param name="index" value="hg19"/>
182 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> 160 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
183 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 161 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
184 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 162 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
163 <param name="set_configuration_switch" value="Customized"/>
164 <param name="callMemMb" value="1000"/>
165 <param name="candidateSmallIndels_check" value="True"/>
166 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
167 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
168 </test>
169 <test>
170 <param name="reference_source_selector" value="cached"/>
171 <param name="index" value="hg19"/>
172 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
173 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
174 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
185 <param name="set_configuration_switch" value="Default_config_file"/> 175 <param name="set_configuration_switch" value="Default_config_file"/>
186 <param name="callMemMb" value="1000"/> 176 <param name="callMemMb" value="1000"/>
187 <param name="candidateSmallIndels_check" value="True"/> 177 <param name="candidateSmallIndels_check" value="True"/>
188 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/> 178 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
179 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
189 </test> 180 </test>
190 <test> 181 <test>
191 <param name="reference_source_selector" value="history"/> 182 <param name="reference_source_selector" value="history"/>
192 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/> 183 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
193 <param name="bam_input_selector" value="tumor_bam"/> 184 <param name="bam_input_selector" value="tumor_bam"/>
194 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 185 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
195 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 186 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
196 <param name="set_configuration_switch" value="Default_config_file"/> 187 <param name="set_configuration_switch" value="Default_config_file"/>
197 <param name="callMemMb" value="1000"/> 188 <param name="callMemMb" value="1000"/>
198 <param name="candidateSV_check" value="True"/> 189 <param name="candidateSV_check" value="True"/>
199 <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="4"/> 190 <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="6"/>
191 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
200 </test> 192 </test>
201 <test> 193 <test>
202 <param name="reference_source_selector" value="history"/> 194 <param name="reference_source_selector" value="history"/>
203 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/> 195 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
204 <param name="bam_input_selector" value="tumor_bam"/> 196 <param name="bam_input_selector" value="tumor_bam"/>
205 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 197 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
206 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 198 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
207 <param name="set_configuration_switch" value="Default_config_file"/> 199 <param name="set_configuration_switch" value="Default_config_file"/>
208 <param name="callMemMb" value="1000"/> 200 <param name="callMemMb" value="1000"/>
209 <param name="candidateSmallIndels_check" value="True"/> 201 <param name="candidateSmallIndels_check" value="True"/>
210 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/> 202 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
211 </test> 203 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
212 </tests> 204 </test>
213 205 </tests>
214 <help><![CDATA[ 206 <help><![CDATA[
215 **Outputs** 207 **Outputs**
216 The primary Manta outputs are a set of VCF 4.1 files. Currently there are 3 VCF files 208 The primary Manta outputs are a set of VCF 4.1 files. Currently there are 3 VCF files
217 created for a germline analysis, and an additional somatic VCF is produced for a 209 created for a germline analysis, and an additional somatic VCF is produced for a
218 tumor/normal subtraction. These files are: 210 tumor/normal subtraction. These files are:
331 most compute intensive scatter-phase tasks of graph 323 most compute intensive scatter-phase tasks of graph
332 creation and candidate generation. 324 creation and candidate generation.
333 325
334 For further info see: https://github.com/Illumina/manta 326 For further info see: https://github.com/Illumina/manta
335 327
336 ]]></help> 328 ]]></help>
337
338 <citations> 329 <citations>
339 <citation type="doi">10.1093/bioinformatics/btv710</citation> 330 <citation type="doi">10.1093/bioinformatics/btv710</citation>
340 </citations> 331 </citations>
341
342 </tool> 332 </tool>