Mercurial > repos > artbio > manta

comparison manta.xml @ 7:555971edd46e draft default tip

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 569d2234f8a576d5c4fdae120a32418c50436ac2
author artbio
date Tue, 20 Feb 2024 08:31:27 +0000
parents cb5691381acb
children
comparison
equal deleted inserted replaced
6:cb5691381acb 7:555971edd46e
1 <tool id="manta" name="Manta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="manta" name="Manta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.</description> 2 <description>Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.</description>
3 <macros> 3 <macros>
4 <import>manta_macros.xml</import> 4 <import>manta_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
8 8
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 @pipefail@ 10 @pipefail@
11 @set_reference_fasta_filename@ 11 @set_reference_fasta_filename@
12 #set run_dir = './MantaWorkflow' 12 #set run_dir = './MantaWorkflow'
13 configManta=\$(which configManta.py) &&
14 PATH=\${configManta/"configManta.py"/}:\$PATH &&
15 printenv &&
13 cp $__tool_directory__/configManta.py.ini configManta.py.ini && 16 cp $__tool_directory__/configManta.py.ini configManta.py.ini &&
14 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": 17 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
15 ln -s '$bam_input.normal_bam_file' normal.bam && 18 ln -s '$bam_input.normal_bam_file' normal.bam &&
16 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai && 19 ln -s '$bam_input.normal_bam_file.metadata.bam_index' normal.bai &&
17 #else if str( $bam_input.bam_input_selector ) == "tumor_bam": 20 #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
24 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file": 27 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file":
25 cp '$set_configuration.CustomConfigFile' ./configManta.py.ini && 28 cp '$set_configuration.CustomConfigFile' ./configManta.py.ini &&
26 #end if 29 #end if
27 #if str( $set_configuration.set_configuration_switch ) == "Customized": 30 #if str( $set_configuration.set_configuration_switch ) == "Customized":
28 rm ./configManta.py.ini && 31 rm ./configManta.py.ini &&
29 python '$__tool_directory__/customConfigManta.py' 32 python2 '$__tool_directory__/customConfigManta.py'
30 --minCandidateVariantSize '$set_configuration.minCandidateVariantSize' 33 --minCandidateVariantSize '$set_configuration.minCandidateVariantSize'
31 --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize' 34 --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize'
32 --minEdgeObservations '$set_configuration.minEdgeObservations' 35 --minEdgeObservations '$set_configuration.minEdgeObservations'
33 --graphNodeMaxEdgeCount '$set_configuration.graphNodeMaxEdgeCount' 36 --graphNodeMaxEdgeCount '$set_configuration.graphNodeMaxEdgeCount'
34 --minCandidateSpanningCount '$set_configuration.minCandidateSpanningCount' 37 --minCandidateSpanningCount '$set_configuration.minCandidateSpanningCount'
110 <param name="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" type="integer" value="1" label="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" help="Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote locations with poor mapping quality. This feature can be enabled/disabled separately for germline and cancer calling below."/> 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."/>
111 <param name="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" type="integer" value="0" label="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" help="Here 'CancerCallingModes' includes tumor-normal subtraction and tumor-only calling. 'GermlineCallingModes' includes all other calling modes."/> 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."/>
112 <param name="useOverlapPairEvidence" type="integer" value="0" label="useOverlapPairEvidence" help="Set if an overlapping read pair will be considered as evidence. Set this value &lt;= 0 to skip overlapping read pairs."/> 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."/>
113 </when> 116 </when>
114 </conditional> 117 </conditional>
115 <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/>
116 <param name="candidateSV_check" type="boolean" label="Unfiltered structural variants" checked="False" 118 <param name="candidateSV_check" type="boolean" label="Unfiltered structural variants" checked="False"
117 help="All unscored structural variant candidates"/> 119 help="All unscored structural variant candidates"/>
118 <param name="candidateSmallIndels_check" type="boolean" label="Unfiltered small indel candidates" checked="False" 120 <param name="candidateSmallIndels_check" type="boolean" label="Unfiltered small indel candidates" checked="False"
119 help="Subset of the unscored candidates, containing only small indel variants"/> 121 help="Subset of the unscored candidates, containing only small indel variants"/>
120 <param name="diploidSV_check" type="boolean" label="Score-filtered variants in diploid model" checked="False" 122 <param name="diploidSV_check" type="boolean" label="Score-filtered variants in diploid model" checked="False"
121 help="Show filtered variants in a diploid (only normal) model. In the case of a tumor/normal subtraction, the scores in this file *do not* 123 help="Show filtered variants in a diploid (only normal) model. In the case of a tumor/normal subtraction, the scores in this file *do not*
122 reflect any information from the tumor sample" /> 124 reflect any information from the tumor sample" />
123 </inputs> 125 </inputs>
124 <outputs> 126 <outputs>
125 <data format="tabular" name="conf_file" label="conf_file.ini" from_work_dir="./configManta.py.ini"> 127 <data format="txt" name="conf_file" label="conf_file.ini" from_work_dir="./configManta.py.ini"/>
126 <filter>config_file_check == True</filter>
127 </data>
128 <data format="vcf_bgzip" name="candidateSV" label="Manta unfiltered variants" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz"> 128 <data format="vcf_bgzip" name="candidateSV" label="Manta unfiltered variants" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz">
129 <filter>candidateSV_check == True</filter> 129 <filter>candidateSV_check == True</filter>
130 </data> 130 </data>
131 <data format="vcf_bgzip" name="candidateSmallIndels" label="Manta unfiltered indels" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz"> 131 <data format="vcf_bgzip" name="candidateSmallIndels" label="Manta unfiltered indels" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz">
132 <filter>candidateSmallIndels_check == True</filter> 132 <filter>candidateSmallIndels_check == True</filter>
137 <data format="vcf_bgzip" name="somaticSV" label="Score-filtered Variants (somatic model)" from_work_dir="MantaWorkflow/results/variants/somaticSV.vcf.gz"> 137 <data format="vcf_bgzip" name="somaticSV" label="Score-filtered Variants (somatic model)" from_work_dir="MantaWorkflow/results/variants/somaticSV.vcf.gz">
138 <filter>bam_input['bam_input_selector'] == 'tumor_bam'</filter> 138 <filter>bam_input['bam_input_selector'] == 'tumor_bam'</filter>
139 </data> 139 </data>
140 </outputs> 140 </outputs>
141 <tests> 141 <tests>
142 <test> 142 <test expect_num_outputs="3">
143 <param name="reference_source_selector" value="cached"/> 143 <param name="reference_source_selector" value="cached"/>
144 <param name="index" value="hg19"/> 144 <param name="index" value="hg19"/>
145 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> 145 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
146 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 146 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
147 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 147 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
148 <param name="set_configuration_switch" value="Default_config_file"/> 148 <param name="set_configuration_switch" value="Default_config_file"/>
149 <param name="callMemMb" value="1000"/> 149 <param name="callMemMb" value="1000"/>
150 <param name="candidateSmallIndels_check" value="True"/> 150 <param name="candidateSmallIndels_check" value="True"/>
151 <output name="conf_file" file="conf_file_1.ini" ftype="txt"/>
151 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/> 152 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
152 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/> 153 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
153 </test> 154 </test>
154 <test> 155 <test expect_num_outputs="3">
155 <param name="reference_source_selector" value="cached"/> 156 <param name="reference_source_selector" value="cached"/>
156 <param name="index" value="hg19"/> 157 <param name="index" value="hg19"/>
157 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> 158 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
158 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 159 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
159 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 160 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
160 <param name="set_configuration_switch" value="Customized"/> 161 <param name="set_configuration_switch" value="Customized"/>
161 <param name="callMemMb" value="1000"/> 162 <param name="callMemMb" value="1000"/>
162 <param name="candidateSmallIndels_check" value="True"/> 163 <param name="candidateSmallIndels_check" value="True"/>
164 <output name="conf_file" file="conf_file_2.ini" ftype="txt"/>
163 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/> 165 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
164 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/> 166 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
165 </test> 167 </test>
166 <test> 168 <test expect_num_outputs="3">
167 <param name="reference_source_selector" value="cached"/> 169 <param name="reference_source_selector" value="cached"/>
168 <param name="index" value="hg19"/> 170 <param name="index" value="hg19"/>
169 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> 171 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
170 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 172 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
171 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 173 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
172 <param name="set_configuration_switch" value="Default_config_file"/> 174 <param name="set_configuration_switch" value="Default_config_file"/>
173 <param name="callMemMb" value="1000"/> 175 <param name="callMemMb" value="1000"/>
174 <param name="candidateSmallIndels_check" value="True"/> 176 <param name="candidateSmallIndels_check" value="True"/>
177 <output name="conf_file" file="conf_file_3.ini" ftype="txt"/>
175 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/> 178 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
176 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/> 179 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
177 </test> 180 </test>
178 <test> 181 <test expect_num_outputs="3">
179 <param name="reference_source_selector" value="history"/> 182 <param name="reference_source_selector" value="history"/>
180 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/> 183 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
181 <param name="bam_input_selector" value="tumor_bam"/> 184 <param name="bam_input_selector" value="tumor_bam"/>
182 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 185 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
183 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 186 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
184 <param name="set_configuration_switch" value="Default_config_file"/> 187 <param name="set_configuration_switch" value="Default_config_file"/>
185 <param name="callMemMb" value="1000"/> 188 <param name="callMemMb" value="1000"/>
186 <param name="candidateSV_check" value="True"/> 189 <param name="candidateSV_check" value="True"/>
190 <output name="conf_file" file="conf_file_4.ini" ftype="txt"/>
187 <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="6"/> 191 <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="6"/>
188 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/> 192 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
189 </test> 193 </test>
190 <test> 194 <test expect_num_outputs="3">
191 <param name="reference_source_selector" value="history"/> 195 <param name="reference_source_selector" value="history"/>
192 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/> 196 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
193 <param name="bam_input_selector" value="tumor_bam"/> 197 <param name="bam_input_selector" value="tumor_bam"/>
194 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 198 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
195 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 199 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
196 <param name="set_configuration_switch" value="Default_config_file"/> 200 <param name="set_configuration_switch" value="Default_config_file"/>
197 <param name="callMemMb" value="1000"/> 201 <param name="callMemMb" value="1000"/>
198 <param name="candidateSmallIndels_check" value="True"/> 202 <param name="candidateSmallIndels_check" value="True"/>
203 <output name="conf_file" file="conf_file_5.ini" ftype="txt"/>
199 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/> 204 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
200 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/> 205 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
201 </test> 206 </test>
202 </tests> 207 </tests>
203 <help><![CDATA[ 208 <help><![CDATA[