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comparison bcftools_call.xml @ 27:1c91646b70a1 draft default tip

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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 07:40:24 +0000
parents 1bdbb4c62840
children
comparison
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26:1bdbb4c62840 27:1c91646b70a1
1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@"> 1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>SNP/indel variant calling from VCF/BCF</description> 2 <description>SNP/indel variant calling from VCF/BCF</description>
3 <macros> 3 <macros>
4 <token name="@EXECUTABLE@">call</token> 4 <token name="@EXECUTABLE@">call</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <xml name="macro_novel_rate"> 6 <xml name="macro_novel_rate">
7 <param name="novel_rate_snp" type="float" value="" optional="true" label="Novel rate for SNPs" 7 <param name="novel_rate_snp" type="float" value="" optional="true" label="Novel rate for SNPs" help="Likelihood of novel mutation for constrained trio calling, see man page for details"/>
8 help="Likelihood of novel mutation for constrained trio calling, see man page for details" /> 8 <param name="novel_rate_del" type="float" value="" optional="true" label="Novel rate for deletions" help="Likelihood of novel mutation for constrained trio calling, see man page for details"/>
9 <param name="novel_rate_del" type="float" value="" optional="true" label="Novel rate for deletions" 9 <param name="novel_rate_ins" type="float" value="" optional="true" label="Novel rate for insertions" help="Likelihood of novel mutation for constrained trio calling, see man page for details"/>
10 help="Likelihood of novel mutation for constrained trio calling, see man page for details" />
11 <param name="novel_rate_ins" type="float" value="" optional="true" label="Novel rate for insertions"
12 help="Likelihood of novel mutation for constrained trio calling, see man page for details" />
13 </xml> 10 </xml>
14 <token name="@NOVEL_RATE@"> 11 <token name="@NOVEL_RATE@">
15 #set $novel_rate = [] 12 #set $novel_rate = []
16 #if str($section.genotypes.novel_rate_snp): 13 #if str($section.genotypes.novel_rate_snp):
17 #silent $novel_rate.append(str($section.genotypes.novel_rate_snp)) 14 #silent $novel_rate.append(str($section.genotypes.novel_rate_snp))
25 #if len($novel_rate) > 0: 22 #if len($novel_rate) > 0:
26 --novel-rate '#echo ','.join($novel_rate)#' 23 --novel-rate '#echo ','.join($novel_rate)#'
27 #end if 24 #end if
28 </token> 25 </token>
29 </macros> 26 </macros>
30 <expand macro="bio_tools" /> 27 <expand macro="bio_tools"/>
31 <expand macro="requirements" /> 28 <expand macro="requirements"/>
32 <expand macro="version_command" /> 29 <expand macro="version_command"/>
33 <command detect_errors="aggressive"><![CDATA[ 30 <command detect_errors="aggressive"><![CDATA[
34 @PREPARE_ENV@
35 @PREPARE_INPUT_FILE@ 31 @PREPARE_INPUT_FILE@
36 #set $section = $sec_consensus_variant_calling.variant_calling 32 #set $section = $sec_consensus_variant_calling.variant_calling
37 #set $targets_path = None 33 #set $targets_path = None
38 #if $section.method == 'multiallelic': 34 #if $section.method == 'multiallelic':
39 #if $section.genotypes.constrain == 'alleles': 35 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
40 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes 36 #end if
41 @PREPARE_TARGETS_FILE@ 37 @PREPARE_TARGETS_FILE@
42 #end if 38
43 #end if
44 #set $section = $sec_restrict 39 #set $section = $sec_restrict
45 @PREPARE_REGIONS_FILE@ 40 @PREPARE_REGIONS_FILE@
46 41
47 bcftools @EXECUTABLE@ 42 bcftools @EXECUTABLE@
48 43
73 #else 68 #else
74 -c 69 -c
75 #if str($section.pval_threshold): 70 #if str($section.pval_threshold):
76 --pval-threshold $section.pval_threshold 71 --pval-threshold $section.pval_threshold
77 #end if 72 #end if
73 @TARGETS@
78 #end if 74 #end if
79 75
80 #set $section = $sec_restrict 76 #set $section = $sec_restrict
81 @REGIONS@ 77 @REGIONS@
82 @SAMPLES@ 78 @SAMPLES@
113 ## Primary Input/Outputs 109 ## Primary Input/Outputs
114 @INPUT_FILE@ 110 @INPUT_FILE@
115 > '$output_file' 111 > '$output_file'
116 ]]></command> 112 ]]></command>
117 <inputs> 113 <inputs>
118 <expand macro="macro_input" /> 114 <expand macro="macro_input"/>
119 <section name="sec_restrict" expanded="false" title="Restrict to"> 115 <section name="sec_restrict" expanded="false" title="Restrict to">
120 <expand macro="macro_restrict" /> 116 <expand macro="macro_region_restrict"/>
121 <expand macro="macro_samples" /> 117 <expand macro="macro_samples"/>
122 </section> 118 </section>
123 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options"> 119 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
124 <conditional name="variant_calling"> 120 <conditional name="variant_calling">
125 <param name="method" type="select" label="Calling method"> 121 <param name="method" type="select" label="Calling method">
126 <option value="multiallelic">Multiallelic and rare-variant caller</option> 122 <option value="multiallelic">Multiallelic and rare-variant caller</option>
132 <option value="none">Do not constrain</option> 128 <option value="none">Do not constrain</option>
133 <option value="alleles">alleles - call genotypes given alleles</option> 129 <option value="alleles">alleles - call genotypes given alleles</option>
134 <option value="trio">trio - call genotypes given the father-mother-child constraint</option> 130 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
135 </param> 131 </param>
136 <when value="none"> 132 <when value="none">
137 <expand macro="macro_restrict" type="target" label_type="Target"> 133 <expand macro="macro_target_restrict_simple" />
138 <expand macro="macro_invert_targets"/>
139 </expand>
140 </when> 134 </when>
141 <when value="alleles"> 135 <when value="alleles">
142 <expand macro="macro_restrictions_file" type="target" label_type="Target" /> 136 <expand macro="macro_restrictions_file" type="target" label_type="Target"/>
143 <expand macro="macro_invert_targets"/> 137 <expand macro="macro_invert_targets"/>
144 <param argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" /> 138 <param argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T"/>
145 </when> 139 </when>
146 <when value="trio"> 140 <when value="trio">
147 <expand macro="macro_restrict" type="target" label_type="Target"> 141 <expand macro="macro_target_restrict_simple"/>
148 <expand macro="macro_invert_targets"/> 142 <expand macro="macro_novel_rate"/>
149 </expand>
150 <expand macro="macro_novel_rate" />
151 </when> 143 </when>
152 </conditional> 144 </conditional>
153 <param argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies"> 145 <param argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
154 <help> 146 <help>
155 <![CDATA[ 147 <![CDATA[
159 <br>##INFO=&lt;ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele"&gt; 151 <br>##INFO=&lt;ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele"&gt;
160 ]]> 152 ]]>
161 </help> 153 </help>
162 <validator type="regex" message="The INFO tags (separated by a comma), e.g. AN,AC">^(\w+,\w+)?$</validator> 154 <validator type="regex" message="The INFO tags (separated by a comma), e.g. AN,AC">^(\w+,\w+)?$</validator>
163 </param> 155 </param>
164 <param argument="--prior" type="float" value="1.1e-3" optional="true" label="Prior" help="Expected substitution rate" /> 156 <param argument="--prior" type="float" value="1.1e-3" optional="true" label="Prior" help="Expected substitution rate"/>
165 <param argument="--gvcf" type="integer" optional="true" label="Output also gVCF blocks of homozygous REF calls" help="The parameter value is the minimum per-sample depth required to include a site in the non-variant block" /> 157 <param argument="--gvcf" type="integer" optional="true" label="Output also gVCF blocks of homozygous REF calls" help="The parameter value is the minimum per-sample depth required to include a site in the non-variant block"/>
166 </when> 158 </when>
167 <when value="consensus"> 159 <when value="consensus">
168 <conditional name="genotypes"> 160 <conditional name="genotypes">
169 <param argument="--constrain" type="select" label="Constrain" help="One of: alleles, trio (see manual)"> 161 <param argument="--constrain" type="select" label="Constrain" help="One of: alleles, trio (see manual)">
170 <option value="none">Do not constrain</option> 162 <option value="none">Do not constrain</option>
171 <option value="trio">trio - call genotypes given the father-mother-child constraint</option> 163 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
172 </param> 164 </param>
173 <when value="none" /> 165 <when value="none"/>
174 <when value="trio"> 166 <when value="trio">
175 <expand macro="macro_novel_rate" /> 167 <expand macro="macro_novel_rate"/>
176 </when> 168 </when>
177 </conditional> 169 </conditional>
178 <expand macro="macro_restrict" type="target" label_type="Target"> 170 <expand macro="macro_target_restrict_simple" />
179 <expand macro="macro_invert_targets" type="target" label_type="Target" /> 171 <param argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT"/>
180 </expand>
181 <param argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" />
182 </when> 172 </when>
183 </conditional> 173 </conditional>
184 </section> 174 </section>
185 <section name="sec_file_format" expanded="false" title="File format Options"> 175 <section name="sec_file_format" expanded="false" title="File format Options">
186 <param argument="--ploidy" type="select" optional="true" label="Select predefined ploidy"> 176 <param argument="--ploidy" type="select" optional="true" label="Select predefined ploidy">
188 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option> 178 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>
189 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option> 179 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
190 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option> 180 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
191 <option value="1">1 - Treat all samples as haploid</option> 181 <option value="1">1 - Treat all samples as haploid</option>
192 </param> 182 </param>
193 <param argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" /> 183 <param argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY"/>
194 <expand macro="macro_restrict" /> 184 <expand macro="macro_region_restrict"/>
195 <expand macro="macro_samples" /> 185 <expand macro="macro_samples"/>
196 </section> 186 </section>
197 <section name="sec_input_output" expanded="false" title="Input/output Options"> 187 <section name="sec_input_output" expanded="false" title="Input/output Options">
198 <param argument="--group-samples" type="boolean" truevalue="--group-samples -" falsevalue="" label="Single Sample Calling" help="Group samples by population for single-sample calling (-G - is the only option implemented so far)" /> 188 <param argument="--group-samples" type="boolean" truevalue="--group-samples -" falsevalue="" label="Single Sample Calling" help="Group samples by population for single-sample calling (-G - is the only option implemented so far)"/>
199 <param argument="--keep-alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep alts" help="Output all alternate alleles present in the alignments even if they do not appear in any of the genotypes" /> 189 <param argument="--keep-alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep alts" help="Output all alternate alleles present in the alignments even if they do not appear in any of the genotypes"/>
200 <param argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample" 190 <param argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample" help="Currently GQ and GP fields are supported">
201 help="Currently GQ and GP fields are supported" >
202 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator> 191 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>
203 </param> 192 </param>
204 <param argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N" /> 193 <param argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N"/>
205 <param argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites"> 194 <param argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites">
206 <option value="indels">indels</option> 195 <option value="indels">indels</option>
207 <option value="snps">snps</option> 196 <option value="snps">snps</option>
208 </param> 197 </param>
209 <param argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" /> 198 <param argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only"/>
210 <expand macro="macro_output_tags"> 199 <expand macro="macro_output_tags">
211 <option value="INFO/PV4">INFO/PV4: P-values for strand bias, baseQ bias, mapQ bias and tail</option> 200 <option value="INFO/PV4">INFO/PV4: P-values for strand bias, baseQ bias, mapQ bias and tail</option>
212 <option value="FORMAT/GQ">FORMAT/GQ: Phred-scaled genotype quality</option> 201 <option value="FORMAT/GQ">FORMAT/GQ: Phred-scaled genotype quality</option>
213 <option value="FORMAT/GP">FORMAT/GP: Phred-scaled genotype posterior probabilities</option> 202 <option value="FORMAT/GP">FORMAT/GP: Phred-scaled genotype posterior probabilities</option>
214 </expand> 203 </expand>
215 </section> 204 </section>
216 <expand macro="macro_select_output_type" /> 205 <expand macro="macro_select_output_type"/>
217 </inputs> 206 </inputs>
218 <outputs> 207 <outputs>
219 <expand macro="macro_vcf_output"/> 208 <expand macro="macro_vcf_output"/>
220 </outputs> 209 </outputs>
221 <tests> 210 <tests>
222 <test> 211 <test>
223 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> 212 <param name="input_file" ftype="vcf" value="mpileup.vcf"/>
224 <param name="method" value="multiallelic" /> 213 <section name="sec_consensus_variant_calling">
225 <param name="variants_only" value="true" /> 214 <conditional name="variant_calling">
226 <param name="output_type" value="v" /> 215 <param name="method" value="multiallelic"/>
227 <output name="output_file"> 216 </conditional>
228 <assert_contents> 217 </section>
229 <has_text text="DP4=2,4,8,11;MQ=49" /> 218 <section name="sec_input_output">
230 </assert_contents> 219 <param name="variants_only" value="true"/>
231 </output> 220 </section>
232 </test> 221 <param name="output_type" value="v"/>
233 <test> 222 <output name="output_file">
234 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> 223 <assert_contents>
235 <param name="method" value="multiallelic" /> 224 <has_text text="DP4=2,4,8,11;MQ=49"/>
236 <param name="gvcf" value="0" /> 225 </assert_contents>
237 <param name="output_type" value="v" /> 226 </output>
238 <output name="output_file"> 227 </test>
239 <assert_contents> 228 <test>
240 <has_text text="MinDP" /> 229 <param name="input_file" ftype="vcf" value="mpileup.vcf"/>
241 <has_text text="DP4=2,4,8,11;MQ=49" /> 230 <section name="sec_consensus_variant_calling">
242 </assert_contents> 231 <conditional name="variant_calling">
243 </output> 232 <param name="method" value="multiallelic"/>
244 </test> 233 <param name="gvcf" value="0"/>
245 <test> 234 </conditional>
246 <param name="input_file" ftype="vcf" value="mpileup.X.vcf" /> 235 </section>
247 <param name="method" value="multiallelic" /> 236 <param name="output_type" value="v"/>
248 <param name="ploidy_file" value="mpileup.ploidy" /> 237 <output name="output_file">
249 <param name="samples_file" value="mpileup.samples" /> 238 <assert_contents>
250 <param name="output_type" value="v" /> 239 <has_text text="MIN_DP"/>
251 <output name="output_file"> 240 <has_text text="DP4=2,4,8,11;MQ=49"/>
252 <assert_contents> 241 </assert_contents>
253 <has_text text="DP4=2,4,8,11;MQ=49" /> 242 </output>
254 </assert_contents> 243 </test>
255 </output> 244 <test>
256 </test> 245 <param name="input_file" ftype="vcf" value="mpileup.X.vcf"/>
257 <test> 246 <section name="sec_consensus_variant_calling">
258 <param name="input_file" ftype="vcf" value="mpileup.X.vcf" /> 247 <conditional name="variant_calling">
259 <param name="method" value="consensus" /> 248 <param name="method" value="multiallelic"/>
260 <param name="output_type" value="v" /> 249 </conditional>
261 <param name="ploidy_file" value="mpileup.ploidy" /> 250 </section>
262 <output name="output_file"> 251 <section name="sec_file_format">
263 <assert_contents> 252 <param name="ploidy_file" value="mpileup.ploidy"/>
264 <has_text text="DP4=2,4,8,11" /> 253 </section>
265 <has_text text="PV4=1,1,1,1" /> 254 <section name="sec_restrict">
255 <param name="samples_file" value="mpileup.samples"/>
256 </section>
257 <param name="output_type" value="v"/>
258 <output name="output_file">
259 <assert_contents>
260 <has_text text="DP4=2,4,8,11;MQ=49"/>
261 </assert_contents>
262 </output>
263 </test>
264 <test>
265 <param name="input_file" ftype="vcf" value="mpileup.X.vcf"/>
266 <section name="sec_consensus_variant_calling">
267 <conditional name="variant_calling">
268 <param name="method" value="consensus"/>
269 </conditional>
270 </section>
271 <param name="output_type" value="v"/>
272 <section name="sec_file_format">
273 <param name="ploidy_file" value="mpileup.ploidy"/>
274 </section>
275 <output name="output_file">
276 <assert_contents>
277 <has_text text="DP4=2,4,8,11"/>
278 <has_text text="PV4=1,1,1,1"/>
266 </assert_contents> 279 </assert_contents>
267 </output> 280 </output>
268 </test> 281 </test>
269 <!-- Test annotate --> 282 <!-- Test annotate -->
270 <test> 283 <test>
271 <param name="input_file" ftype="vcf" value="mpileup.X.vcf" /> 284 <param name="input_file" ftype="vcf" value="mpileup.X.vcf"/>
272 <param name="method" value="consensus" /> 285 <section name="sec_consensus_variant_calling">
273 <param name="output_type" value="v" /> 286 <conditional name="variant_calling">
274 <param name="ploidy_file" value="mpileup.ploidy" /> 287 <param name="method" value="consensus"/>
288 </conditional>
289 </section>
290 <param name="output_type" value="v"/>
291 <section name="sec_file_format">
292 <param name="ploidy_file" value="mpileup.ploidy"/>
293 </section>
275 <section name="sec_input_output"> 294 <section name="sec_input_output">
276 <param name="output_tags" value="INFO/PV4"/> 295 <param name="output_tags" value="INFO/PV4"/>
277 </section> 296 </section>
278 <output name="output_file"> 297 <output name="output_file">
279 <assert_contents> 298 <assert_contents>
280 <has_text text="DP4=2,4,8,11" /> 299 <has_text text="DP4=2,4,8,11"/>
281 <has_text text="PV4=1,1,1,1" /> 300 <has_text text="PV4=1,1,1,1"/>
282 </assert_contents> 301 </assert_contents>
283 </output> 302 </output>
284 <assert_command> 303 <assert_command>
285 <has_text text="--annotate" /> 304 <has_text text="--annotate"/>
286 </assert_command> 305 </assert_command>
287 </test> 306 </test>
288 <!-- Test region overlap--> 307 <!-- Test region overlap-->
289 <test> 308 <test>
290 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> 309 <param name="input_file" ftype="vcf" value="mpileup.vcf"/>
291 <param name="method" value="multiallelic" /> 310 <section name="sec_consensus_variant_calling">
292 <param name="variants_only" value="true" /> 311 <conditional name="variant_calling">
293 <param name="output_type" value="v" /> 312 <param name="method" value="multiallelic"/>
313 </conditional>
314 </section>
315 <section name="sec_input_output">
316 <param name="variants_only" value="true"/>
317 </section>
318 <param name="output_type" value="v"/>
294 <section name="sec_restrict"> 319 <section name="sec_restrict">
295 <param name="regions_overlap" value="1"/> 320 <conditional name="regions">
296 </section> 321 <param name="regions_src" value="regions" />
297 <output name="output_file"> 322 <repeat name="region_specs">
298 <assert_contents> 323 <param name="chrom" value="17" />
299 <has_text text="DP4=2,4,8,11;MQ=49" /> 324 </repeat>
325 </conditional>
326 </section>
327 <output name="output_file">
328 <assert_contents>
329 <has_text text="DP4=2,4,8,11;MQ=49"/>
300 </assert_contents> 330 </assert_contents>
301 </output> 331 </output>
302 <assert_command> 332 <assert_command>
303 <has_text text="--regions-overlap" /> 333 <has_text text="--regions-overlap"/>
304 </assert_command> 334 </assert_command>
305 </test> 335 </test>
306 <!-- Test group samples option--> 336 <!-- Test group samples option-->
307 <test> 337 <test>
308 <param name="input_file" ftype="vcf" value="mpileup.AD.vcf" /> 338 <param name="input_file" ftype="vcf" value="mpileup.AD.vcf"/>
309 <param name="method" value="multiallelic" /> 339 <section name="sec_consensus_variant_calling">
310 <param name="output_type" value="v" /> 340 <conditional name="variant_calling">
341 <param name="method" value="multiallelic"/>
342 </conditional>
343 </section>
344 <param name="output_type" value="v"/>
311 <section name="sec_input_output"> 345 <section name="sec_input_output">
312 <param name="group_samples" value="true" /> 346 <param name="group_samples" value="true"/>
313 </section> 347 </section>
314 <output name="output_file"> 348 <output name="output_file">
315 <assert_contents> 349 <assert_contents>
316 <has_text text="bcftools_callCommand=call -m --prior 0.0011 --group-samples - " /> 350 <has_text text="bcftools_callCommand=call -m --prior 0.0011 --group-samples - "/>
317 <has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" /> 351 <has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37"/>
318 </assert_contents> 352 </assert_contents>
319 </output> 353 </output>
320 </test> 354 </test>
321 <test> 355 <test>
322 <!-- Test targets-file option--> 356 <!-- Test targets-file option-->
323 <param name="input_file" ftype="vcf" value="mpileup.AD.vcf" /> 357 <param name="input_file" ftype="vcf" value="mpileup.AD.vcf"/>
324 <param name="method" value="multiallelic" /> 358 <section name="sec_consensus_variant_calling">
325 <param name="output_type" value="v" /> 359 <conditional name="variant_calling">
360 <param name="method" value="multiallelic"/>
361 </conditional>
362 </section>
363 <param name="output_type" value="v"/>
326 <section name="sec_consensus_variant_calling"> 364 <section name="sec_consensus_variant_calling">
327 <conditional name="variant_calling"> 365 <conditional name="variant_calling">
328 <conditional name="genotypes"> 366 <conditional name="genotypes">
329 <conditional name="targets"> 367 <conditional name="targets">
330 <param name="targets_src" value="targets_file"/> 368 <param name="targets_src" value="targets_file"/>
333 </conditional> 371 </conditional>
334 </conditional> 372 </conditional>
335 </section> 373 </section>
336 <output name="output_file"> 374 <output name="output_file">
337 <assert_contents> 375 <assert_contents>
338 <has_text text="--targets-file" /> 376 <has_text text="--targets-file"/>
339 <not_has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" /> 377 <not_has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37"/>
340 </assert_contents> 378 </assert_contents>
341 </output> 379 </output>
342 </test> 380 </test>
343 </tests> 381 </tests>
344 <help><![CDATA[ 382 <help><![CDATA[
358 @REGIONS_HELP@ 396 @REGIONS_HELP@
359 @TARGETS_HELP@ 397 @TARGETS_HELP@
360 398
361 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 399 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
362 400
363 @BCFTOOLS_WIKI@ 401 @BCFTOOLS_HOWTOS@
364 ]]> 402 ]]>
365 </help> 403 </help>
366 <expand macro="citations" /> 404 <expand macro="citations"/>
367 </tool> 405 </tool>