Mercurial > repos > artbio > manta

annotate manta.xml @ 5:f55d45b0c6d1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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"
artbio
parents:
diff changeset
2
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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"
artbio
parents:
diff changeset
4
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
5 <macros>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
6 <import>manta_macros.xml</import>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
7 </macros>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
8 <expand macro="requirements"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
9 <expand macro="stdio"/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
10
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
12 @VERSION@
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
13 @pipefail@
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
14 @set_reference_fasta_filename@
3
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
15 #set run_dir = './MantaWorkflow'
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
16 cp $__tool_directory__/configManta.py.ini configManta.py.ini &&
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
17 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
3
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
18 ln -s '$bam_input.normal_bam_file' normal.bam &&
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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"
artbio
parents:
diff changeset
20 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
3
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
21 ln -s '$bam_input.normal_bam_file' normal.bam &&
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
22 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai &&
3
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
23 ln -s '$bam_input.tumor_bam_file' tumor.bam &&
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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"
artbio
parents:
diff changeset
25 #end if
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
26
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
27 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file":
3
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
28 cp '$set_configuration.CustomConfigFile' ./configManta.py.ini &&
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
29 #end if
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
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"
artbio
parents: 4
diff changeset
31 rm ./configManta.py.ini &&
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
32 python $__tool_directory__/customConfigManta.py
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
33 --minCandidateVariantSize '$set_configuration.minCandidateVariantSize'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
34 --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
35 --minEdgeObservations '$set_configuration.minEdgeObservations'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
36 --graphNodeMaxEdgeCount '$set_configuration.graphNodeMaxEdgeCount'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
37 --minCandidateSpanningCount '$set_configuration.minCandidateSpanningCount'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
38 --minScoredVariantSize '$set_configuration.minScoredVariantSize'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
39 --minDiploidVariantScore '$set_configuration.minDiploidVariantScore'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
40 --minPassDiploidVariantScore '$set_configuration.minPassDiploidVariantScore'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
41 --minPassDiploidGTScore '$set_configuration.minPassDiploidGTScore'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
42 --minSomaticScore '$set_configuration.minSomaticScore'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
43 --minPassSomaticScore '$set_configuration.minPassSomaticScore'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
44 --enableRemoteReadRetrievalForInsertionsInGermlineCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
45 --enableRemoteReadRetrievalForInsertionsInCancerCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
46 --useOverlapPairEvidence '$set_configuration.useOverlapPairEvidence' &&
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
47 #end if
3
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
48
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
49 configManta.py --referenceFasta='${reference_fasta_filename}'
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
50 --config='./configManta.py.ini'
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
51 #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"
artbio
parents: 0
diff changeset
52 --bam='normal.bam'
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
53 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
54 --bam='normal.bam'
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
55 --tumorBam='tumor.bam'
d648e40c6da9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
artbio
parents: 0
diff changeset
56 #end if
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
57 --runDir='${run_dir}'
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
58 --scanSizeMb=${advanced.scanSizeMb}
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
59 --callMemMb=${advanced.callMemMb} &&
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
60
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
61 python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4}
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
62
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
63 ]]></command>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
64
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
65 <inputs>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
66 <expand macro="reference_source_conditional" />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
67 <conditional name="bam_input">
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
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">
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
69 <option value="not_tumor_bam">Normal</option>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
70 <option value="tumor_bam">Normal + Tumor</option>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
71 </param>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
72 <when value="not_tumor_bam">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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)." />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
74 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
75 <when value='tumor_bam'>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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)." />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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)." />
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
78 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
79 </conditional>
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
80 <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional parameters" >
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
81 <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"
artbio
parents:
diff changeset
82 <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"
artbio
parents:
diff changeset
83 <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"
artbio
parents:
diff changeset
84 </param>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
85 <section name="advanced" title="Advanced options" expanded="false">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
86 <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"
artbio
parents:
diff changeset
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)" />
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
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
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
89 </section>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
90 <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
91 <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?">
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
92 <option value="Default_config_file">Default Manta Configuration File</option>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
93 <option value="Custom_config_file">Upload your Own Configuration File</option>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
94 <option value="Customized">Customize a Configuration File using this Galaxy Form</option>
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
95 </param>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
96 <when 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
97 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
98 <when value="Custom_config_file">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
99 <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"
artbio
parents:
diff changeset
100 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
101 <when value="Customized">
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
103 <param name="rnaMinCandidateVariantSize" type="integer" value="1000" label="rnaMinCandidateVariantSize" help="Separate option (to provide different default) used for runs in RNA-mode."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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'."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
111 <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"
artbio
parents:
diff changeset
112 <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"
artbio
parents:
diff changeset
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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
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."/>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
116 </when>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
117 </conditional>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
118 <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
119 <param name="candidateSV_check" type="boolean" label="Unfiltered structural variants" checked="False"
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
120 help="All unscored structural variant candidates"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
121 <param name="candidateSmallIndels_check" type="boolean" label="Unfiltered small indel candidates" checked="False"
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
122 help="Subset of the unscored candidates, containing only small indel variants"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
123 <param name="diploidSV_check" type="boolean" label="Score-filtered variants in diploid model" checked="False"
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
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*
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
125 reflect any information from the tumor sample" />
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
126 </inputs>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
127 <outputs>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
128 <data format="tabular" name="conf_file" label="conf_file.ini" from_work_dir="./configManta.py.ini">
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
129 <filter>config_file_check == True</filter>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
130 </data>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
131 <data format="vcf_bgzip" name="candidateSV" label="Manta unfiltered variants" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz">
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
132 <filter>candidateSV_check == True</filter>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
133 </data>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
134 <data format="vcf_bgzip" name="candidateSmallIndels" label="Manta unfiltered indels" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz">
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
135 <filter>candidateSmallIndels_check == True</filter>
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
136 </data>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
137 <data format="vcf_bgzip" name="diploidSV" label="Score-filtered Variants (diploid model)" from_work_dir="MantaWorkflow/results/variants/diploidSV.vcf.gz">
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
138 <filter>diploidSV_check == True</filter>
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
139 </data>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
140 <data format="vcf_bgzip" name="somaticSV" label="Score-filtered Variants (somatic model)" from_work_dir="MantaWorkflow/results/variants/somaticSV.vcf.gz">
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
141 <filter>bam_input['bam_input_selector'] == 'tumor_bam'</filter>
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
142 </data>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
143 </outputs>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
144 <tests>
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
145 <test>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
146 <param name="reference_source_selector" value="cached"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
147 <param name="index" value="hg19"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
148 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
149 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
150 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
151 <param name="set_configuration_switch" value="Default_config_file"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
152 <param name="callMemMb" value="1000"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
153 <param name="candidateSmallIndels_check" value="True"/>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
154 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
155 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
156 </test>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
157 <test>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
158 <param name="reference_source_selector" value="cached"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
159 <param name="index" value="hg19"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
160 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
161 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
162 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
163 <param name="set_configuration_switch" value="Customized"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
164 <param name="callMemMb" value="1000"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
165 <param name="candidateSmallIndels_check" value="True"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
166 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
167 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
168 </test>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
169 <test>
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
170 <param name="reference_source_selector" value="cached"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
171 <param name="index" value="hg19"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
172 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
173 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
174 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
175 <param name="set_configuration_switch" value="Default_config_file"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
176 <param name="callMemMb" value="1000"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
177 <param name="candidateSmallIndels_check" value="True"/>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
178 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
179 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
180 </test>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
181 <test>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
182 <param name="reference_source_selector" value="history"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
183 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
184 <param name="bam_input_selector" value="tumor_bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
185 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
186 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
187 <param name="set_configuration_switch" value="Default_config_file"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
188 <param name="callMemMb" value="1000"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
189 <param name="candidateSV_check" value="True"/>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
190 <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="6"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
191 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
192 </test>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
193 <test>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
194 <param name="reference_source_selector" value="history"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
195 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
196 <param name="bam_input_selector" value="tumor_bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
197 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
198 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
199 <param name="set_configuration_switch" value="Default_config_file"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
200 <param name="callMemMb" value="1000"/>
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
201 <param name="candidateSmallIndels_check" value="True"/>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
202 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
203 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
204 </test>
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
205 </tests>
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
206 <help><![CDATA[
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
207 **Outputs**
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
208 The primary Manta outputs are a set of VCF 4.1 files. Currently there are 3 VCF files
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
209 created for a germline analysis, and an additional somatic VCF is produced for a
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
210 tumor/normal subtraction. These files are:
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
211
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
212 - diploidSV.vcf.gz
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
213 SVs and indels scored and genotyped under a diploid model for the set of samples in a
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
214 joint diploid sample analysis or for the normal sample in a tumor/normal subtraction
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
215 analysis. **In the case of a tumor/normal subtraction, the scores in this file do not
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
216 reflect any information from the tumor sample.**
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
217
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
218 - somaticSV.vcf.gz
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
219 SVs and indels scored under a somatic variant model. This file will only be produced
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
220 if a tumor sample alignment file is supplied during configuration
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
221
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
222 - candidateSV.vcf.gz
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
223 Unscored SV and indel candidates. Only a minimal amount of supporting evidence is
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
224 required for an SV to be entered as a candidate in this file. An SV or indel must be a
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
225 candidate to be considered for scoring, therefore an SV cannot appear in the other VCF
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
226 outputs if it is not present in this file. Note that by default this file includes
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
227 indels of size 8 and larger. The smallest indels in this set are intended to be passed
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
228 on to a small variant caller without scoring by manta itself (by default manta scoring
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
229 starts at size 50).
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
230
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
231 - candidateSmallIndels.vcf.gz
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
232 Subset of the candidateSV.vcf.gz file containing only simple insertion and deletion
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
233 variants less than the minimum scored variant size (50 by default). Passing this file
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
234 to a small variant caller will provide continuous coverage over all indel sizes when
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
235 the small variant caller and manta outputs are evaluated together. Alternate small
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
236 indel candidate sets can be parsed out of the candidateSV.vcf.gz file if this
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
237 candidate set is not appropriate.
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
238
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
239 For tumor-only analysis, Manta will produce an additional VCF:
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
240
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
241 - tumorSV.vcf.gz
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
242 Subset of the candidateSV.vcf.gz file after removing redundant candidates and small
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
243 indels less than the minimum scored variant size (50 by default). The SVs are not
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
244 scored, but include additional details: (1) paired and split read supporting evidence
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
245 counts for each allele (2) a subset of the filters from the scored tumor-normal model
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
246 are applied to the single tumor case to improve precision.
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
247
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
248 **Manta helps**
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
249 This script configures the Manta SV analysis pipeline.
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
250 You must specify a BAM or CRAM file for at least one sample.
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
251 Configuration will produce a workflow run script which
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
252 can execute the workflow on a single node or through
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
253 sge and resume any interrupted execution.
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
254
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
255 **Options**
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
256 --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
257 -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
258 --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
259 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
260 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
261 --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
262 **Workflow options**
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
263 --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
264 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
265 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
266 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
267 default)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
268 --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
269 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
270 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
271 --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
272 --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
273 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
274 --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
275 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
276 --referenceFasta=FILE
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
277 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
278 --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
279 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
280 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
281 MantaWorkflow)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
282 --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
283 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
284 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
285 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
286 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
287 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
288 (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
289 **Extended options**
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
290 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
291 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
parents:
diff changeset
292 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
293 specified
4
d09254e37c68 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
artbio
parents: 3
diff changeset
294
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
295 --existingAlignStatsFile=FILE
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
296 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
297 alignment stats calculation.
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
298 --useExistingChromDepths
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
299 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
300 --candidateBins=candidateBins
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
301 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
parents:
diff changeset
302 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
303 --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
304 --generateEvidenceBam
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
305 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
parents:
diff changeset
306 --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
307 --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
308 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
309 12)
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
310 --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
311 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
312 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
313 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
314 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
315 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
316 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
317 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
318 --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
319 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
320 --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
321 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
322 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
323 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
324 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
325
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
326 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
parents:
diff changeset
327
5
f55d45b0c6d1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 86427647db100383faa432008b58e768b56ac416"
artbio
parents: 4
diff changeset
328 ]]></help>
0
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
329 <citations>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
330 <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
331 </citations>
42ba283a0fe2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
artbio
parents:
diff changeset
332 </tool>