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comparison manta.xml @ 4:d09254e37c68 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
author artbio
date Mon, 08 Jun 2020 03:11:56 -0400
parents d648e40c6da9
children f55d45b0c6d1
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3:d648e40c6da9 4:d09254e37c68
57 --scanSizeMb=${advanced.scanSizeMb} 57 --scanSizeMb=${advanced.scanSizeMb}
58 --callMemMb=${advanced.callMemMb} && 58 --callMemMb=${advanced.callMemMb} &&
59 59
60 ln -s -f '${run_dir}/runWorkflow.py' '${run_manta_workflow}' && 60 ln -s -f '${run_dir}/runWorkflow.py' '${run_manta_workflow}' &&
61 ln -s -f './configManta.py.ini' '${set_conf_file}' && 61 ln -s -f './configManta.py.ini' '${set_conf_file}' &&
62 python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4} && 62 python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4}
63 cp '${run_dir}/results/variants/candidateSV.vcf.gz' '${out_vcf1}' &&
64 cp '${run_dir}/results/variants/diploidSV.vcf.gz' '${out_vcf2}' &&
65 cp '${run_dir}/results/variants/candidateSmallIndels.vcf.gz' '${out_vcf3}'
66 63
67 ]]></command> 64 ]]></command>
68 65
69 <inputs> 66 <inputs>
70 <expand macro="reference_source_conditional" /> 67 <expand macro="reference_source_conditional" />
83 <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)." /> 80 <param name="normal_bam_file" type="data" format="bam" label="select normal BAM" help="Select the files you wish to send to Manta (normal sample, it must be in BAM format)." />
84 <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)." /> 81 <param name="tumor_bam_file" type="data" format="bam" label="select tumor BAM" help="Select the files you wish to send to Manta (tumor sample, it must be in BAM format)." />
85 </when> 82 </when>
86 </conditional> 83 </conditional>
87 84
88 <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional outputs" help="Additional parameters."> 85 <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional parameters" >
89 <option value="exome">Set options for WES input: turn off depth filters</option> 86 <option value="exome">Set options for WES input: turn off depth filters</option>
90 <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option> 87 <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option>
91 <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option> 88 <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option>
92 </param> 89 </param>
93 90
94 <section name="advanced" title="Advanced options" expanded="false"> 91 <section name="advanced" title="Advanced options" expanded="false">
95 92
96 <param name="callMemMb" type="integer" value="8000" label="Set default task memory requirements" help="The maximum memory size to assign to tasks" /> 93 <param name="callMemMb" type="integer" value="8000" label="Set default task memory requirements" help="The maximum memory size to assign to tasks" />
97 <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)" /> 94 <param name="scanSizeMb" type="integer" value="12" label="Set maximum sequence region size" help="The maximum sequence region size (in megabases) scanned by each task during SV Locus graph generation. (default: 12)" />
98 <param name="retainTempFiles" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Keep all temporary files" help="Click yes so all temporary files (for workflow debugging) will be kept."/> 95 <!-- <param name="generateEvidenceBam" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Generate a bam of supporting reads for all SVs" help="Click yes for generating a BAM of supporting reads for all SVs."/> -->
99 <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."/>
100 96
101 </section> 97 </section>
102 98
103 <!-- <expand macro="manta_configuration"/> --> 99 <!-- <expand macro="manta_configuration"/> -->
104 100
105 <conditional name="set_configuration"> 101 <conditional name="set_configuration">
106 <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?"> 102 <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?">
107 <option value="Default_config_file">Default</option> 103 <option value="Default_config_file">Default Manta Configuration File</option>
108 <option value="Custom_config_file">Upload a different config file</option> 104 <option value="Custom_config_file">Upload your Own Configuration File</option>
109 <option value="Customized">Customize the options</option> 105 <option value="Customized">Customize a Configuration File using this Galaxy Form</option>
110 </param> 106 </param>
111 <when value="Default_config_file"> 107 <when value="Default_config_file">
112 </when> 108 </when>
113 <when value="Custom_config_file"> 109 <when value="Custom_config_file">
114 <param format="ini" name="CustomConfigFile" type="data" label="config file"/> 110 <param format="ini" name="CustomConfigFile" type="data" label="config file"/>
131 </when> 127 </when>
132 </conditional> 128 </conditional>
133 129
134 <param name="runworkflow_file_check" type="boolean" label="output manta run_workflow file" checked="False" help="Show run_workflow file on history"/> 130 <param name="runworkflow_file_check" type="boolean" label="output manta run_workflow file" checked="False" help="Show run_workflow file on history"/>
135 <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/> 131 <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/>
136 <param name="O1_check" type="boolean" label="snvs filtred" checked="False" help="Show filtred snvs"/> 132 <param name="candidateSV_check" type="boolean" label="Unscored candidate SV and indels" checked="False"
137 <param name="O2_check" type="boolean" label="indels filtred" checked="False" help="Show filtred indels"/> 133 help="Show unfiltered structural variants"/>
138 <param name="O3_check" type="boolean" label="all snvs" checked="False" help="Show snvs"/> 134 <param name="candidateSmallIndels_check" type="boolean" label="all snvs" checked="False"
139 135 help="Subset of the Unscored candidate SV and indels, containing only simple insertion and deletion variants"/>
136 <param name="diploidSV_check" type="boolean" label="filtered variants in diploid model" checked="False"
137 help="Show filtered variants in a diploid (only normal) model. In the case of a tumor/normal subtraction, the scores in this file *do not*
138 reflect any information from the tumor sample" />
139 <param name="somaticSV_check" type="boolean" label="SVs and indels scored under a somatic variant model" checked="False"
140 help="This file will only be produced if a tumor sample alignment file is supplied during configuration"/>
140 </inputs> 141 </inputs>
141 142
142 <outputs> 143 <outputs>
143
144 <data format="txt" name="run_manta_workflow" label="Parameters for running Manta"> 144 <data format="txt" name="run_manta_workflow" label="Parameters for running Manta">
145 <filter>runworkflow_file_check == True</filter> 145 <filter>runworkflow_file_check == True</filter>
146 </data> 146 </data>
147 147
148 <data format="tabular" name="set_conf_file" label="conf_file.ini"> 148 <data format="tabular" name="set_conf_file" label="conf_file.ini">
149 <filter>config_file_check == True</filter> 149 <filter>config_file_check == True</filter>
150 </data> 150 </data>
151 <data format="vcf_bgzip" name="out_vcf1" label="${tool.name} on ${on_string} (Generating the candidateSV.vcf file)" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz"> 151 <data format="vcf_bgzip" name="candidateSV" label="Manta unfiltered SVs" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz">
152 <filter>O1_check == True</filter> 152 <filter>candidateSV_check == True</filter>
153 </data> 153 </data>
154 <data format="vcf_bgzip" name="out_vcf2" label="${tool.name} on ${on_string} (Generating the diploidSV.vcf file)" from_work_dir="MantaWorkflow/results/variants/diploidSV.vcf.gz"> 154 <data format="vcf_bgzip" name="candidateSmallIndels" label="Manta unfiltered Small Indels" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz">
155 <filter>O2_check == True</filter> 155 <filter>candidateSmallIndels_check == True</filter>
156 </data> 156 </data>
157 <data format="vcf_bgzip" name="out_vcf3" label="${tool.name} on ${on_string} (Generating the candidateSmallIndels.vcf file)" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz"> 157 <data format="vcf_bgzip" name="diploidSV" label="Manta SVs (diploid model)" from_work_dir="MantaWorkflow/results/variants/diploidSV.vcf.gz">
158 <filter>O3_check == True</filter> 158 <filter>diploidSV_check == True</filter>
159 </data>
160 <data format="vcf_bgzip" name="somaticSV" label="Manta SVs (somatic model)" from_work_dir="MantaWorkflow/results/variants/somaticSV.vcf.gz">
161 <filter>somaticSV_check == True</filter>
159 </data> 162 </data>
160 </outputs> 163 </outputs>
161 164
162 <tests> 165 <tests>
163 <test> 166 <test>
164 <conditional name="reference_source"> 167 <param name="reference_source_selector" value="cached"/>
165 <param name="reference_source_selector" value="cached"/> 168 <param name="index" value="hg19"/>
166 <param name="index" value="hg19"/> 169 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
167 </conditional> 170 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
168 171 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
169 <conditional name="bam_input"> 172 <param name="set_configuration_switch" value="Default_config_file"/>
170 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> 173 <param name="callMemMb" value="1000"/>
171 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 174 <param name="candidateSmallIndels_check" value="True"/>
172 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 175 <param name="somaticSV_check" value="True"/>
173 </conditional> 176 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
174 177 <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="4"/>
175 <conditional name="set_configuration"> 178 </test>
176 <param name="set_configuration_switch" value="Default_config_file"/> 179 <test>
177 </conditional> 180 <param name="reference_source_selector" value="cached"/>
178 <param name="callMemMb" value="1000"/> 181 <param name="index" value="hg19"/>
179 <param name="O3_check" value="True"/> 182 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
180 <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/> 183 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
181 </test> 184 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
182 <test> 185 <param name="set_configuration_switch" value="Default_config_file"/>
183 <conditional name="reference_source"> 186 <param name="callMemMb" value="1000"/>
184 <param name="reference_source_selector" value="history"/> 187 <param name="candidateSmallIndels_check" value="True"/>
185 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/> 188 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
186 </conditional> 189 </test>
187 190 <test>
188 <conditional name="bam_input"> 191 <param name="reference_source_selector" value="history"/>
189 <param name="bam_input_selector" value="tumor_bam"/> 192 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
190 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 193 <param name="bam_input_selector" value="tumor_bam"/>
191 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 194 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
192 </conditional> 195 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
193 196 <param name="set_configuration_switch" value="Default_config_file"/>
194 <conditional name="set_configuration"> 197 <param name="callMemMb" value="1000"/>
195 <param name="set_configuration_switch" value="Default_config_file"/> 198 <param name="candidateSV_check" value="True"/>
196 </conditional> 199 <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="4"/>
197 <param name="callMemMb" value="1000"/> 200 </test>
198 <param name="O1_check" value="True"/> 201 <test>
199 <output name="out_vcf1" file="candidateSV.vcf.gz" decompress="true" lines_diff="4"/> 202 <param name="reference_source_selector" value="history"/>
200 </test> 203 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
201 <test> 204 <param name="bam_input_selector" value="tumor_bam"/>
202 <conditional name="reference_source"> 205 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
203 <param name="reference_source_selector" value="history"/> 206 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
204 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/> 207 <param name="set_configuration_switch" value="Default_config_file"/>
205 </conditional> 208 <param name="callMemMb" value="1000"/>
206 209 <param name="candidateSmallIndels_check" value="True"/>
207 <conditional name="bam_input"> 210 <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
208 <param name="bam_input_selector" value="tumor_bam"/> 211 </test>
209 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> 212 </tests>
210 <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> 213
211 </conditional>
212
213 <conditional name="set_configuration">
214 <param name="set_configuration_switch" value="Default_config_file"/>
215 </conditional>
216 <param name="callMemMb" value="1000"/>
217 <param name="O3_check" value="True"/>
218 <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
219 </test>
220 </tests>
221
222 <help><![CDATA[ 214 <help><![CDATA[
223 **Manta** 215 **Outputs**
224 This script configures the Manta SV analysis pipeline. 216 The primary Manta outputs are a set of VCF 4.1 files. Currently there are 3 VCF files
225 You must specify a BAM or CRAM file for at least one sample. 217 created for a germline analysis, and an additional somatic VCF is produced for a
226 Configuration will produce a workflow run script which 218 tumor/normal subtraction. These files are:
227 can execute the workflow on a single node or through 219
228 sge and resume any interrupted execution. 220 - diploidSV.vcf.gz
221 SVs and indels scored and genotyped under a diploid model for the set of samples in a
222 joint diploid sample analysis or for the normal sample in a tumor/normal subtraction
223 analysis. **In the case of a tumor/normal subtraction, the scores in this file do not
224 reflect any information from the tumor sample.**
225
226 - somaticSV.vcf.gz
227 SVs and indels scored under a somatic variant model. This file will only be produced
228 if a tumor sample alignment file is supplied during configuration
229
230 - candidateSV.vcf.gz
231 Unscored SV and indel candidates. Only a minimal amount of supporting evidence is
232 required for an SV to be entered as a candidate in this file. An SV or indel must be a
233 candidate to be considered for scoring, therefore an SV cannot appear in the other VCF
234 outputs if it is not present in this file. Note that by default this file includes
235 indels of size 8 and larger. The smallest indels in this set are intended to be passed
236 on to a small variant caller without scoring by manta itself (by default manta scoring
237 starts at size 50).
238
239 - candidateSmallIndels.vcf.gz
240 Subset of the candidateSV.vcf.gz file containing only simple insertion and deletion
241 variants less than the minimum scored variant size (50 by default). Passing this file
242 to a small variant caller will provide continuous coverage over all indel sizes when
243 the small variant caller and manta outputs are evaluated together. Alternate small
244 indel candidate sets can be parsed out of the candidateSV.vcf.gz file if this
245 candidate set is not appropriate.
246
247 For tumor-only analysis, Manta will produce an additional VCF:
248
249 - tumorSV.vcf.gz
250 Subset of the candidateSV.vcf.gz file after removing redundant candidates and small
251 indels less than the minimum scored variant size (50 by default). The SVs are not
252 scored, but include additional details: (1) paired and split read supporting evidence
253 counts for each allele (2) a subset of the filters from the scored tumor-normal model
254 are applied to the single tumor case to improve precision.
255
256 **Manta helps**
257 This script configures the Manta SV analysis pipeline.
258 You must specify a BAM or CRAM file for at least one sample.
259 Configuration will produce a workflow run script which
260 can execute the workflow on a single node or through
261 sge and resume any interrupted execution.
229 262
230 **Options** 263 **Options**
231 --version show program's version number and exit 264 --version show program's version number and exit
232 -h, --help show this help message and exit 265 -h, --help show this help message and exit
233 --config=FILE provide a configuration file to override defaults in 266 --config=FILE provide a configuration file to override defaults in
264 **Extended options** 297 **Extended options**
265 These options are either unlikely to be reset after initial site 298 These options are either unlikely to be reset after initial site
266 configuration or only of interest for workflow development/debugging. 299 configuration or only of interest for workflow development/debugging.
267 They will not be printed here if a default exists unless --allHelp is 300 They will not be printed here if a default exists unless --allHelp is
268 specified 301 specified
302
269 --existingAlignStatsFile=FILE 303 --existingAlignStatsFile=FILE
270 Pre-calculated alignment statistics file. Skips 304 Pre-calculated alignment statistics file. Skips
271 alignment stats calculation. 305 alignment stats calculation.
272 --useExistingChromDepths 306 --useExistingChromDepths
273 Use pre-calculated chromosome depths. 307 Use pre-calculated chromosome depths.