Mercurial > repos > artbio > manta

comparison manta.xml @ 3:d648e40c6da9 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 3b3617515f0e59c35849939c26e4891f02c4de0b"
author artbio
date Sun, 07 Jun 2020 16:43:54 -0400
parents 42ba283a0fe2
children d09254e37c68
comparison
equal deleted inserted replaced
2:6a69e5d7c21f 3:d648e40c6da9
10 10
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 @VERSION@ 12 @VERSION@
13 @pipefail@ 13 @pipefail@
14 @set_reference_fasta_filename@ 14 @set_reference_fasta_filename@
15 15 #set run_dir = './MantaWorkflow'
16 #import os 16 cp $__tool_directory__/configManta.py.ini configManta.py.ini &&
17 #import random
18 #set job_dir=os.getcwd()
19 #set run_dir = job_dir + '/MantaWorkflow_' + (' ' + str(random.randint(1,100000))).strip()
20 #set config_file = $__tool_directory__ + '/configManta.py.ini'
21 #set config_file_custom = $__tool_directory__ + '/customized.ini'
22 #set $input_normal = 'normal.bam'
23 #set $input_tumor = 'tumor.bam'
24
25 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": 17 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
26 ln -s '$bam_input.normal_bam_file' $input_normal && 18 ln -s '$bam_input.normal_bam_file' normal.bam &&
27 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai && 19 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai &&
28 #else if str( $bam_input.bam_input_selector ) == "tumor_bam": 20 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
29 ln -s '$bam_input.normal_bam_file' $input_normal && 21 ln -s '$bam_input.normal_bam_file' normal.bam &&
30 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 &&
31 ln -s '$bam_input.tumor_bam_file' $input_tumor && 23 ln -s '$bam_input.tumor_bam_file' tumor.bam &&
32 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 &&
33 #end if 25 #end if
34 26
35 cp ${config_file} ${config_file_custom} &&
36
37 #if str( $set_configuration.set_configuration_switch ) == "Customized": 27 #if str( $set_configuration.set_configuration_switch ) == "Customized":
38 sed -i 's/minCandidateVariantSize = 8/minCandidateVariantSize = $set_configuration.minCandidateVariantSize/' ${config_file_custom} && 28 sed -i 's/minCandidateVariantSize = 8/minCandidateVariantSize = $set_configuration.minCandidateVariantSize/' ./configManta.py.ini &&
39 sed -i 's/rnaMinCandidateVariantSize = 1000/rnaMinCandidateVariantSize = $set_configuration.rnaMinCandidateVariantSize/' ${config_file_custom} && 29 sed -i 's/rnaMinCandidateVariantSize = 1000/rnaMinCandidateVariantSize = $set_configuration.rnaMinCandidateVariantSize/' ./configManta.py.ini &&
40 sed -i 's/minEdgeObservations = 3/minEdgeObservations = $set_configuration.minEdgeObservations/' ${config_file_custom} && 30 sed -i 's/minEdgeObservations = 3/minEdgeObservations = $set_configuration.minEdgeObservations/' ./configManta.py.ini &&
41 sed -i 's/graphNodeMaxEdgeCount = 10/graphNodeMaxEdgeCount = $set_configuration.graphNodeMaxEdgeCount/' ${config_file_custom} && 31 sed -i 's/graphNodeMaxEdgeCount = 10/graphNodeMaxEdgeCount = $set_configuration.graphNodeMaxEdgeCount/' ./configManta.py.ini &&
42 sed -i 's/minCandidateSpanningCount = 3/minCandidateSpanningCount = $set_configuration.minCandidateSpanningCount/' ${config_file_custom} && 32 sed -i 's/minCandidateSpanningCount = 3/minCandidateSpanningCount = $set_configuration.minCandidateSpanningCount/' ./configManta.py.ini &&
43 sed -i 's/minScoredVariantSize = 50/minScoredVariantSize = $set_configuration.minScoredVariantSize/' ${config_file_custom} && 33 sed -i 's/minScoredVariantSize = 50/minScoredVariantSize = $set_configuration.minScoredVariantSize/' ./configManta.py.ini &&
44 sed -i 's/minDiploidVariantScore = 10/minDiploidVariantScore = $set_configuration.minDiploidVariantScore/' ${config_file_custom} && 34 sed -i 's/minDiploidVariantScore = 10/minDiploidVariantScore = $set_configuration.minDiploidVariantScore/' ./configManta.py.ini &&
45 sed -i 's/minPassDiploidVariantScore = 20/minPassDiploidVariantScore = $set_configuration.minPassDiploidVariantScore/' ${config_file_custom} && 35 sed -i 's/minPassDiploidVariantScore = 20/minPassDiploidVariantScore = $set_configuration.minPassDiploidVariantScore/' ./configManta.py.ini &&
46 sed -i 's/minPassDiploidGTScore = 15/minPassDiploidGTScore = $set_configuration.minPassDiploidGTScore/' ${config_file_custom} && 36 sed -i 's/minPassDiploidGTScore = 15/minPassDiploidGTScore = $set_configuration.minPassDiploidGTScore/' ./configManta.py.ini &&
47 sed -i 's/minSomaticScore = 10/minSomaticScore = $set_configuration.minSomaticScore/' ${config_file_custom} && 37 sed -i 's/minSomaticScore = 10/minSomaticScore = $set_configuration.minSomaticScore/' ./configManta.py.ini &&
48 sed -i 's/minPassSomaticScore = 30/minPassSomaticScore = $set_configuration.minPassSomaticScore/' ${config_file_custom} && 38 sed -i 's/minPassSomaticScore = 30/minPassSomaticScore = $set_configuration.minPassSomaticScore/' ./configManta.py.ini &&
49 sed -i 's/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes/' ${config_file_custom} && 39 sed -i 's/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1/enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes/' ./configManta.py.ini &&
50 sed -i 's/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes/' ${config_file_custom} && 40 sed -i 's/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0/enableRemoteReadRetrievalForInsertionsInCancerCallingModes = $set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes/' ./configManta.py.ini &&
51 sed -i 's/useOverlapPairEvidence = 0/useOverlapPairEvidence = $set_configuration.useOverlapPairEvidence/' ${config_file_custom} && 41 sed -i 's/useOverlapPairEvidence = 0/useOverlapPairEvidence = $set_configuration.useOverlapPairEvidence/' ./configManta.py.ini &&
52 #end if 42 #end if
53 43
54 configManta.py
55 --referenceFasta='${reference_fasta_filename}'
56
57 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file": 44 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file":
58 #set config_file = $set_configuration.CustomConfigFile 45 cp '$set_configuration.CustomConfigFile' ./configManta.py.ini &&
59 #else if str( $set_configuration.set_configuration_switch ) == "Customized":
60 #set config_file = config_file_custom
61 #end if 46 #end if
62 47
63 --config=${config_file} 48 configManta.py --referenceFasta='${reference_fasta_filename}'
64 49 --config='./configManta.py.ini'
65 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": 50 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
66 --bam=$input_normal 51 --bam='normal.bam'
67 #else if str( $bam_input.bam_input_selector ) == "tumor_bam": 52 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
68 --bam=$input_normal 53 --bam='normal.bam'
69 --tumorBam=$input_tumor 54 --tumorBam='tumor.bam'
70 #end if 55 #end if
71 56 --runDir='${run_dir}'
72 --runDir='${run_dir}' 57 --scanSizeMb=${advanced.scanSizeMb}
73 --scanSizeMb=${advanced.scanSizeMb} 58 --callMemMb=${advanced.callMemMb} &&
74 --callMemMb=${advanced.callMemMb} &&
75 59
76 ln -s -f '${run_dir}/runWorkflow.py' '${run_manta_workflow}' && 60 ln -s -f '${run_dir}/runWorkflow.py' '${run_manta_workflow}' &&
77 ln -s -f '${config_file}' '${set_conf_file}' && 61 ln -s -f './configManta.py.ini' '${set_conf_file}' &&
78 python2 '${run_dir}/runWorkflow.py' -m local -j 8 && 62 python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4} &&
79 ln -s -f '${run_dir}/results/variants/candidateSV.vcf.gz' '${out_vcf1}' && 63 cp '${run_dir}/results/variants/candidateSV.vcf.gz' '${out_vcf1}' &&
80 ln -s -f '${run_dir}/results/variants/diploidSV.vcf.gz' '${out_vcf2}' && 64 cp '${run_dir}/results/variants/diploidSV.vcf.gz' '${out_vcf2}' &&
81 ln -s -f '${run_dir}/results/variants/candidateSmallIndels.vcf.gz' '${out_vcf3}' 65 cp '${run_dir}/results/variants/candidateSmallIndels.vcf.gz' '${out_vcf3}'
82 66
83 ]]></command> 67 ]]></command>
84 68
85 <inputs> 69 <inputs>
86 <expand macro="reference_source_conditional" /> 70 <expand macro="reference_source_conditional" />
176 </outputs> 160 </outputs>
177 161
178 <tests> 162 <tests>
179 <test> 163 <test>
180 <conditional name="reference_source"> 164 <conditional name="reference_source">
165 <param name="reference_source_selector" value="cached"/>
166 <param name="index" value="hg19"/>
167 </conditional>
168
169 <conditional name="bam_input">
170 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
171 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
172 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
173 </conditional>
174
175 <conditional name="set_configuration">
176 <param name="set_configuration_switch" value="Default_config_file"/>
177 </conditional>
178 <param name="callMemMb" value="1000"/>
179 <param name="O3_check" value="True"/>
180 <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
181 </test>
182 <test>
183 <conditional name="reference_source">
181 <param name="reference_source_selector" value="history"/> 184 <param name="reference_source_selector" value="history"/>
182 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/> 185 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
183 </conditional> 186 </conditional>
184 187
185 <conditional name="bam_input"> 188 <conditional name="bam_input">
201 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/> 204 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
202 </conditional> 205 </conditional>
203 206
204 <conditional name="bam_input"> 207 <conditional name="bam_input">
205 <param name="bam_input_selector" value="tumor_bam"/> 208 <param name="bam_input_selector" value="tumor_bam"/>
206 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
207 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
208 </conditional>
209
210 <conditional name="set_configuration">
211 <param name="set_configuration_switch" value="Default_config_file"/>
212 </conditional>
213 <param name="callMemMb" value="1000"/>
214 <param name="O3_check" value="True"/>
215 <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
216 </test>
217 <test>
218 <conditional name="reference_source">
219 <param name="reference_source_selector" value="cached"/>
220 <param name="index" value="hg19"/>
221 </conditional>
222
223 <conditional name="bam_input">
224 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
225 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 209 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
226 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 210 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
227 </conditional> 211 </conditional>
228 212
229 <conditional name="set_configuration"> 213 <conditional name="set_configuration">