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comparison bcftools_call.xml @ 17:22637b1a55bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 13:00:06 +0000
parents d267bcfdc8fe
children 1001172b5089
comparison
equal deleted inserted replaced
16:c37b684e7f4e 17:22637b1a55bf
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>SNP/indel variant calling from VCF/BCF</description> 3 <description>SNP/indel variant calling from VCF/BCF</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">call</token> 5 <token name="@EXECUTABLE@">call</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <xml name="macro_novel_rate"> 7 <xml name="macro_novel_rate">
91 --ploidy-file '${section.ploidy_file}' 91 --ploidy-file '${section.ploidy_file}'
92 #end if 92 #end if
93 93
94 ## Input/output section 94 ## Input/output section
95 #set $section = $sec_input_output 95 #set $section = $sec_input_output
96 ${section.group_samples}
96 ${section.keep_alts} 97 ${section.keep_alts}
97 #if $section.format_fields: 98 #if $section.format_fields:
98 --format-fields '${section.format_fields}' 99 --format-fields '${section.format_fields}'
99 #end if 100 #end if
100 ${section.keep_masked_ref} 101 ${section.keep_masked_ref}
101 #if $section.skip_variants: 102 #if $section.skip_variants:
102 --skip-variants ${section.skip_variants} 103 --skip-variants ${section.skip_variants}
103 #end if 104 #end if
104 ${section.variants_only} 105 ${section.variants_only}
106
107 #if $section.output_tags
108 --annotate $section.output_tags
109 #end if
105 110
106 @OUTPUT_TYPE@ 111 @OUTPUT_TYPE@
107 @THREADS@ 112 @THREADS@
108 113
109 ## Primary Input/Outputs 114 ## Primary Input/Outputs
182 <param name="ploidy_file" argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" /> 187 <param name="ploidy_file" argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
183 <expand macro="macro_restrict" /> 188 <expand macro="macro_restrict" />
184 <expand macro="macro_samples" /> 189 <expand macro="macro_samples" />
185 </section> 190 </section>
186 <section name="sec_input_output" expanded="false" title="Input/output Options"> 191 <section name="sec_input_output" expanded="false" title="Input/output Options">
192 <param name="group_samples" 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)" />
187 <param name="keep_alts" 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" /> 193 <param name="keep_alts" 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" />
188 <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample" 194 <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"
189 help="Currently GQ and GP fields are supported" > 195 help="Currently GQ and GP fields are supported" >
190 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator> 196 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>
191 </param> 197 </param>
193 <param name="skip_variants" argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites"> 199 <param name="skip_variants" argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites">
194 <option value="indels">indels</option> 200 <option value="indels">indels</option>
195 <option value="snps">snps</option> 201 <option value="snps">snps</option>
196 </param> 202 </param>
197 <param name="variants_only" argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" /> 203 <param name="variants_only" argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" />
204 <expand macro="macro_output_tags">
205 <option value="INFO/PV4">INFO/PV4: P-values for strand bias, baseQ bias, mapQ bias and tail</option>
206 <option value="FORMAT/GQ">FORMAT/GQ: Phred-scaled genotype quality</option>
207 <option value="FORMAT/GP">FORMAT/GP: Phred-scaled genotype posterior probabilities</option>
208 </expand>
198 </section> 209 </section>
199 <expand macro="macro_select_output_type" /> 210 <expand macro="macro_select_output_type" />
200 </inputs> 211 </inputs>
201 <outputs> 212 <outputs>
202 <expand macro="macro_vcf_output"/> 213 <expand macro="macro_vcf_output"/>
247 <has_text text="DP4=2,4,8,11" /> 258 <has_text text="DP4=2,4,8,11" />
248 <has_text text="PV4=1,1,1,1" /> 259 <has_text text="PV4=1,1,1,1" />
249 </assert_contents> 260 </assert_contents>
250 </output> 261 </output>
251 </test> 262 </test>
263 <!-- Test annotate -->
264 <test>
265 <param name="input_file" ftype="vcf" value="mpileup.X.vcf" />
266 <param name="method" value="consensus" />
267 <param name="output_type" value="v" />
268 <param name="ploidy_file" value="mpileup.ploidy" />
269 <section name="sec_input_output">
270 <param name="output_tags" value="INFO/PV4"/>
271 </section>
272 <output name="output_file">
273 <assert_contents>
274 <has_text text="DP4=2,4,8,11" />
275 <has_text text="PV4=1,1,1,1" />
276 </assert_contents>
277 </output>
278 <assert_command>
279 <has_text text="--annotate" />
280 </assert_command>
281 </test>
282 <!-- Test region overlap-->
283 <test>
284 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
285 <param name="method" value="multiallelic" />
286 <param name="variants_only" value="true" />
287 <param name="output_type" value="v" />
288 <section name="sec_restrict">
289 <param name="regions_overlap" value="1"/>
290 </section>
291 <output name="output_file">
292 <assert_contents>
293 <has_text text="DP4=2,4,8,11;MQ=49" />
294 </assert_contents>
295 </output>
296 <assert_command>
297 <has_text text="--regions-overlap" />
298 </assert_command>
299 </test>
300 <!-- Test group samples option-->
301 <test>
302 <param name="input_file" ftype="vcf" value="mpileup.AD.vcf" />
303 <param name="method" value="multiallelic" />
304 <param name="output_type" value="v" />
305 <section name="sec_input_output">
306 <param name="group_samples" value="true" />
307 </section>
308 <output name="output_file">
309 <assert_contents>
310 <has_text text="bcftools_callCommand=call -m --prior 0.0011 --group-samples - " />
311 <has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" />
312 </assert_contents>
313 </output>
314 </test>
252 </tests> 315 </tests>
253 <help><![CDATA[ 316 <help><![CDATA[
254 ================================== 317 ==================================
255 bcftools @EXECUTABLE@ 318 bcftools @EXECUTABLE@
256 ================================== 319 ==================================