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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:52:52 +0000
parents 4904c06618a9
children
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24:4904c06618a9 25:9a099033525d
2 <description>Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values</description> 2 <description>Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values</description>
3 <macros> 3 <macros>
4 <token name="@EXECUTABLE@">cnv</token> 4 <token name="@EXECUTABLE@">cnv</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="bio_tools" /> 7 <expand macro="bio_tools"/>
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <expand macro="matplotlib_requirement" /> 9 <expand macro="matplotlib_requirement"/>
10 </expand> 10 </expand>
11 <expand macro="version_command" /> 11 <expand macro="version_command"/>
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@
14 @PREPARE_INPUT_FILE@ 13 @PREPARE_INPUT_FILE@
15 #set $section = $sec_restrict 14 #set $section = $sec_restrict
16 @PREPARE_TARGETS_FILE@ 15 @PREPARE_TARGETS_FILE@
17 @PREPARE_REGIONS_FILE@ 16 @PREPARE_REGIONS_FILE@
18 17
92 #end if 91 #end if
93 92
94 ]]> 93 ]]>
95 </command> 94 </command>
96 <inputs> 95 <inputs>
97 <expand macro="macro_input" /> 96 <expand macro="macro_input"/>
98 <param argument="-s" name="query_sample" type="text" label="Query Sample" optional="True" help="The name (as used in the input) of the query sample in the input. Can be ommitted if, and only if, there is only one sample in the input." /> 97 <param argument="-s" name="query_sample" type="text" label="Query Sample" optional="True" help="The name (as used in the input) of the query sample in the input. Can be ommitted if, and only if, there is only one sample in the input."/>
99 <param argument="-c" name="control_sample" type="text" label="Control Sample" optional="True" help="The name (as used in the input) of an optional control sample to compare against. Note: The pairwise calling mode represents the real strength of the tool as it helps to reduce the number of false calls and also allows one to distinguish between normal and novel copy number variation." /> 98 <param argument="-c" name="control_sample" type="text" label="Control Sample" optional="True" help="The name (as used in the input) of an optional control sample to compare against. Note: The pairwise calling mode represents the real strength of the tool as it helps to reduce the number of false calls and also allows one to distinguish between normal and novel copy number variation."/>
100 <expand macro="macro_AF_file" /> 99 <expand macro="macro_AF_file"/>
101 <conditional name="plotting"> 100 <conditional name="plotting">
102 <param name="generate_plots" type="select" label="Plot results?"> 101 <param name="generate_plots" type="select" label="Plot results?">
103 <option value="all">Yes, plot results for all chromosomes</option> 102 <option value="all">Yes, plot results for all chromosomes</option>
104 <option value="some">Yes, but plot only chromosomes with above-threshold quality of CNV status estimate</option> 103 <option value="some">Yes, but plot only chromosomes with above-threshold quality of CNV status estimate</option>
105 <option value="none">No, do not generate plots</option> 104 <option value="none">No, do not generate plots</option>
106 </param> 105 </param>
107 <when value="all"> 106 <when value="all">
108 <param name="plot_threshold" type="hidden" value="0" /> 107 <param name="plot_threshold" type="hidden" value="0"/>
109 </when> 108 </when>
110 <when value="some"> 109 <when value="some">
111 <param argument="-p" name="plot_threshold" type="float" value="0" 110 <param argument="-p" name="plot_threshold" type="float" value="0" label="Plot Threshold" help="Plot aberrant chromosomes with quality at least 'float'"/>
112 label="Plot Threshold"
113 help="Plot aberrant chromosomes with quality at least 'float'" />
114 </when> 111 </when>
115 <when value="none" /> 112 <when value="none"/>
116 </conditional> 113 </conditional>
117 <section name="sec_restrict" expanded="false" title="Restrict to"> 114 <section name="sec_restrict" expanded="false" title="Restrict to">
118 <expand macro="macro_restrict" /> 115 <expand macro="macro_region_restrict"/>
119 <expand macro="macro_restrict" type="target" label_type="Target" /> 116 <expand macro="macro_target_restrict"/>
120 </section> 117 </section>
121 <section name="sec_hmm" expanded="false" title="HMM Options"> 118 <section name="sec_hmm" expanded="false" title="HMM Options">
122 <param argument="--aberrant" name="aberrant_query" type="float" value="1" min="0" max="1" 119 <param argument="--aberrant" name="aberrant_query" type="float" value="1" min="0" max="1" label="Estimated purity of the query sample" help="Estimate of the fractional contribution of the desired query tissue to the (possibly control-contaminated) query sample (default: 1 = no contamination with control tissue)"/>
123 label="Estimated purity of the query sample" 120 <param argument="--aberrant" name="aberrant_control" type="float" value="1" min="0" max="1" label="Estimated purity of the control sample" help="Estimate of the fractional contribution of the desired control tissue to the (possibly query-contaminated) control sample (default: 1 = no contamination with query tissue)"/>
124 help="Estimate of the fractional contribution of the desired query tissue to the (possibly control-contaminated) query sample (default: 1 = no contamination with control tissue)" />
125 <param argument="--aberrant" name="aberrant_control" type="float" value="1" min="0" max="1"
126 label="Estimated purity of the control sample"
127 help="Estimate of the fractional contribution of the desired control tissue to the (possibly query-contaminated) control sample (default: 1 = no contamination with query tissue)" />
128 <conditional name="aberrant_optimization"> 121 <conditional name="aberrant_optimization">
129 <param name="do_optimize" type="select" 122 <param name="do_optimize" type="select" label="Adjust sample purity estimates based on data?" help="Instead of treating your specified estimates of the sample purities as fixed values, the tool can use them as starting values for an iterative optimization that tries to estimate the sample purities from the data. Note: With estimate optimization enabled the final estimates will be reported as cell fraction (CF) estimates in the summary report.">
130 label="Adjust sample purity estimates based on data?"
131 help="Instead of treating your specified estimates of the sample purities as fixed values, the tool can use them as starting values for an iterative optimization that tries to estimate the sample purities from the data. Note: With estimate optimization enabled the final estimates will be reported as cell fraction (CF) estimates in the summary report.">
132 <option value="no">No, leave sample purities as specified</option> 123 <option value="no">No, leave sample purities as specified</option>
133 <option value="yes">Yes, adjust purity estimates</option> 124 <option value="yes">Yes, adjust purity estimates</option>
134 </param> 125 </param>
135 <when value="no" /> 126 <when value="no"/>
136 <when value="yes"> 127 <when value="yes">
137 <param argument="--optimize" name="lower_bound" type="float" value="0.3" min="1e-9" max="1" 128 <param argument="--optimize" name="lower_bound" type="float" value="0.3" min="1e-9" max="1" label="Lower bound for adjusted estimate" help="Constrains the final adjusted purity estimates not to be smaller than this value."/>
138 label="Lower bound for adjusted estimate"
139 help="Constrains the final adjusted purity estimates not to be smaller than this value." />
140 </when> 129 </when>
141 </conditional> 130 </conditional>
142 <conditional name="score_usage"> 131 <conditional name="score_usage">
143 <param name="compute_on" type="select" label="Use BAF and LRR annotations to call CNVs?" 132 <param name="compute_on" type="select" label="Use BAF and LRR annotations to call CNVs?" help="Using LRR information in addition to BAF values is the default and helps in dealing with random noise in the data. However, the tool is also able to call CNVs from BAF values alone in case your input does not feature LRR information.">
144 help="Using LRR information in addition to BAF values is the default and helps in dealing with random noise in the data. However, the tool is also able to call CNVs from BAF values alone in case your input does not feature LRR information.">
145 <option value="baf+lrr">Yes (requires input with both BAF and LRR subfields)</option> 133 <option value="baf+lrr">Yes (requires input with both BAF and LRR subfields)</option>
146 <option value="baf">No, use BAF values exclusively</option> 134 <option value="baf">No, use BAF values exclusively</option>
147 </param> 135 </param>
148 <when value="baf+lrr"> 136 <when value="baf+lrr">
149 <param argument="--BAF-weight" name="baf_weight" type="float" value="1" min="0" max="1" 137 <param argument="--BAF-weight" name="baf_weight" type="float" value="1" min="0" max="1" label="Baf Weight" help="relative contribution from BAF"/>
150 label="Baf Weight" help="relative contribution from BAF" /> 138 <param argument="--BAF-dev" name="baf_dev_query" type="float" value="0.04" min="0" max="1" label="Query sample BAF deviation" help="Expected BAF deviation in the query sample (default: 0.04)"/>
151 139 <param argument="--BAF-dev" name="baf_dev_control" type="float" value="0.04" min="0" max="1" label="Control sample BAF deviation" help="Expected BAF deviation in the control sample (default: 0.04)"/>
152 <param argument="--BAF-dev" name="baf_dev_query" type="float" value="0.04" min="0" max="1" 140 <param argument="--LRR-weight" name="lrr_weight" type="float" value="0.2" min="0" max="1" label="LRR Weight" help="Relative contribution from LRR. This option can have a big effect on the number of calls produced. With truly random noise (such as in simulated data), the value should be set high (1.0), but in the presence of systematic noise when LRR values are not informative, lower values result in cleaner calls (default: 0.2)."/>
153 label="Query sample BAF deviation" 141 <param argument="--LRR-dev" name="lrr_dev_query" type="float" value="0.2" min="0" max="1" label="Query sample LRR Deviation" help="Expected LRR deviation in the query sample (default: 0.2)"/>
154 help="Expected BAF deviation in the query sample (default: 0.04)" /> 142 <param argument="--LRR-dev" name="lrr_dev_control" type="float" value="0.2" min="0" max="1" label="Control sample LRR Deviation" help="Expected LRR deviation in the control sample (default: 0.2)"/>
155 <param argument="--BAF-dev" name="baf_dev_control" type="float" value="0.04" min="0" max="1" 143 <param argument="--LRR-smooth-win" name="lrr_smooth_win" type="integer" value="10" label="LRR Smoothing Window" help="Window of LRR moving average smoothing (default: 10)"/>
156 label="Control sample BAF deviation"
157 help="Expected BAF deviation in the control sample (default: 0.04)" />
158
159 <param argument="--LRR-weight" name="lrr_weight" type="float" value="0.2" min="0" max="1"
160 label="LRR Weight"
161 help="Relative contribution from LRR. This option can have a big effect on the number of calls produced. With truly random noise (such as in simulated data), the value should be set high (1.0), but in the presence of systematic noise when LRR values are not informative, lower values result in cleaner calls (default: 0.2)." />
162 <param argument="--LRR-dev" name="lrr_dev_query" type="float" value="0.2" min="0" max="1"
163 label="Query sample LRR Deviation"
164 help="Expected LRR deviation in the query sample (default: 0.2)" />
165 <param argument="--LRR-dev" name="lrr_dev_control" type="float" value="0.2" min="0" max="1"
166 label="Control sample LRR Deviation"
167 help="Expected LRR deviation in the control sample (default: 0.2)" />
168 <param argument="--LRR-smooth-win" name="lrr_smooth_win" type="integer" value="10"
169 label="LRR Smoothing Window"
170 help="Window of LRR moving average smoothing (default: 10)" />
171 </when> 144 </when>
172 <when value="baf"> 145 <when value="baf">
173 <param argument="--BAF-dev" name="baf_dev_query" type="float" value="0.04" min="0" max="1" 146 <param argument="--BAF-dev" name="baf_dev_query" type="float" value="0.04" min="0" max="1" label="Query sample BAF deviation" help="Expected BAF deviation in the query sample (default: 0.04)"/>
174 label="Query sample BAF deviation" 147 <param argument="--BAF-dev" name="baf_dev_control" type="float" value="0.04" min="0" max="1" label="Control sample BAF deviation" help="Expected BAF deviation in the control sample (default: 0.04)"/>
175 help="Expected BAF deviation in the query sample (default: 0.04)" /> 148 <param name="baf_weight" type="hidden" value="1"/>
176 <param argument="--BAF-dev" name="baf_dev_control" type="float" value="0.04" min="0" max="1" 149 <param name="lrr_weight" type="hidden" value="0"/>
177 label="Control sample BAF deviation"
178 help="Expected BAF deviation in the control sample (default: 0.04)" />
179 <param name="baf_weight" type="hidden" value="1" />
180 <param name="lrr_weight" type="hidden" value="0" />
181 </when> 150 </when>
182 </conditional> 151 </conditional>
183 <param argument="--err-prob" type="float" value="1e-4" label="Err Prob" help="Uniform error probability" /> 152 <param argument="--err-prob" type="float" value="1e-4" label="Err Prob" help="Uniform error probability"/>
184 <param argument="--same-prob" type="float" value="0.5" min="0" max="1" label="Same Prob"> 153 <param argument="--same-prob" type="float" value="0.5" min="0" max="1" label="Same Prob">
185 <help> 154 <help>
186 The prior probability of the query and the control sample being the same. 155 The prior probability of the query and the control sample being the same.
187 Setting to 0 calls both independently, setting to 1 forces the same copy number state in both. (default: 0.5) 156 Setting to 0 calls both independently, setting to 1 forces the same copy number state in both. (default: 0.5)
188 </help> 157 </help>
202 <filter>plotting['generate_plots'] != 'none'</filter> 171 <filter>plotting['generate_plots'] != 'none'</filter>
203 </data> 172 </data>
204 </outputs> 173 </outputs>
205 <tests> 174 <tests>
206 <test expect_num_outputs="3"> 175 <test expect_num_outputs="3">
207 <param name="input_file" ftype="vcf" value="cnv.vcf" /> 176 <param name="input_file" ftype="vcf" value="cnv.vcf"/>
208 <output name="output_summary" file="cnv_summary.tab" compare="re_match" /> 177 <output name="output_summary" file="cnv_summary.tab" compare="re_match"/>
209 </test> 178 </test>
210 <test expect_num_outputs="2"> 179 <test expect_num_outputs="2">
211 <param name="input_file" ftype="vcf" value="cnv.vcf" /> 180 <param name="input_file" ftype="vcf" value="cnv.vcf"/>
212 <conditional name="plotting"> 181 <conditional name="plotting">
213 <param name="generate_plots" value="none" /> 182 <param name="generate_plots" value="none"/>
214 </conditional> 183 </conditional>
215 <output name="output_summary" file="cnv_summary.tab" compare="re_match" /> 184 <output name="output_summary" file="cnv_summary.tab" compare="re_match"/>
216 </test> 185 </test>
217 <test expect_num_outputs="3"> 186 <test expect_num_outputs="3">
218 <param name="input_file" ftype="vcf" value="cnv.vcf" /> 187 <param name="input_file" ftype="vcf" value="cnv.vcf"/>
219 <param name="query_sample" value="test" /> 188 <param name="query_sample" value="test"/>
220 <param name="control_sample" value="test" /> 189 <param name="control_sample" value="test"/>
221 <output name="output_summary" file="cnv_pairwise_summary.tab" compare="re_match" /> 190 <output name="output_summary" file="cnv_pairwise_summary.tab" compare="re_match"/>
222 </test> 191 </test>
223 <test expect_num_outputs="2"> 192 <test expect_num_outputs="2">
224 <param name="input_file" ftype="vcf" value="cnv_baf_only.vcf" /> 193 <param name="input_file" ftype="vcf" value="cnv_baf_only.vcf"/>
225 <conditional name="plotting"> 194 <conditional name="plotting">
226 <param name="generate_plots" value="none" /> 195 <param name="generate_plots" value="none"/>
227 </conditional> 196 </conditional>
228 <conditional name="score_usage"> 197 <section name="sec_hmm">
229 <param name="compute_on" value="baf" /> 198 <conditional name="score_usage">
230 </conditional> 199 <param name="compute_on" value="baf"/>
231 <output name="output_summary" file="cnv_summary.tab" compare="re_match" /> 200 </conditional>
201 </section>
202 <output name="output_summary" file="cnv_summary.tab" compare="re_match"/>
232 </test> 203 </test>
233 <!-- Test region overlap option --> 204 <!-- Test region overlap option -->
234 <test expect_num_outputs="3"> 205 <test expect_num_outputs="3">
235 <param name="input_file" ftype="vcf" value="cnv.vcf" /> 206 <param name="input_file" ftype="vcf" value="cnv.vcf"/>
236 <section name="sec_restrict"> 207 <section name="sec_restrict">
237 <param name="regions_overlap" value="1"/> 208 <conditional name="regions">
209 <param name="regions_src" value="regions" />
210 <repeat name="region_specs">
211 <param name="chrom" value="10" />
212 </repeat>
213 <repeat name="region_specs">
214 <param name="chrom" value="11" />
215 </repeat>
216 </conditional>
238 </section> 217 </section>
239 <output name="output_summary" file="cnv_summary.tab" compare="re_match" /> 218 <output name="output_summary" file="cnv_summary.tab" compare="re_match"/>
240 <assert_command> 219 <assert_command>
241 <has_text text="--regions-overlap" /> 220 <has_text text="--regions-overlap"/>
242 </assert_command> 221 </assert_command>
243 </test> 222 </test>
244 </tests> 223 </tests>
245 <help><![CDATA[ 224 <help><![CDATA[
246 ===================================== 225 =====================================
253 @REGIONS_HELP@ 232 @REGIONS_HELP@
254 @TARGETS_HELP@ 233 @TARGETS_HELP@
255 234
256 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 235 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
257 236
258 @BCFTOOLS_WIKI@ 237 @BCFTOOLS_HOWTOS@
259 ]]> 238 ]]>
260 </help> 239 </help>
261 <expand macro="citations" /> 240 <expand macro="citations"/>
262 </tool> 241 </tool>