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comparison bcftools_call.xml @ 22:bf06b66ab5c2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 868f4386992de55d25da197660a43a913a09c8df
author iuc
date Wed, 14 Aug 2024 16:43:44 +0000
parents 1001172b5089
children 07396b423218
comparison
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21:1001172b5089 22:bf06b66ab5c2
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@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy4" 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">
133 <option value="none">Do not constrain</option> 133 <option value="none">Do not constrain</option>
134 <option value="alleles">alleles - call genotypes given alleles</option> 134 <option value="alleles">alleles - call genotypes given alleles</option>
135 <option value="trio">trio - call genotypes given the father-mother-child constraint</option> 135 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
136 </param> 136 </param>
137 <when value="none"> 137 <when value="none">
138 <expand macro="macro_restrict" type="target" label_type="Target" /> 138 <expand macro="macro_restrict" type="target" label_type="Target">
139 <expand macro="macro_invert_targets"/>
140 </expand>
139 </when> 141 </when>
140 <when value="alleles"> 142 <when value="alleles">
141 <expand macro="macro_restrictions_file" type="target" label_type="Target" /> 143 <expand macro="macro_restrictions_file" type="target" label_type="Target" />
144 <expand macro="macro_invert_targets"/>
142 <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 <param argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" />
143 </when> 146 </when>
144 <when value="trio"> 147 <when value="trio">
145 <expand macro="macro_restrict" type="target" label_type="Target" /> 148 <expand macro="macro_restrict" type="target" label_type="Target">
149 <expand macro="macro_invert_targets"/>
150 </expand>
146 <expand macro="macro_novel_rate" /> 151 <expand macro="macro_novel_rate" />
147 </when> 152 </when>
148 </conditional> 153 </conditional>
149 <param argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies"> 154 <param argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
150 <help> 155 <help>
169 <when value="none" /> 174 <when value="none" />
170 <when value="trio"> 175 <when value="trio">
171 <expand macro="macro_novel_rate" /> 176 <expand macro="macro_novel_rate" />
172 </when> 177 </when>
173 </conditional> 178 </conditional>
174 <expand macro="macro_restrict" type="target" label_type="Target" /> 179 <expand macro="macro_restrict" type="target" label_type="Target">
180 <expand macro="macro_invert_targets" type="target" label_type="Target" />
181 </expand>
175 <param argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" /> 182 <param argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" />
176 </when> 183 </when>
177 </conditional> 184 </conditional>
178 </section> 185 </section>
179 <section name="sec_file_format" expanded="false" title="File format Options"> 186 <section name="sec_file_format" expanded="false" title="File format Options">
310 <has_text text="bcftools_callCommand=call -m --prior 0.0011 --group-samples - " /> 317 <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" /> 318 <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> 319 </assert_contents>
313 </output> 320 </output>
314 </test> 321 </test>
322 <test>
323 <!-- Test targets-file option-->
324 <param name="input_file" ftype="vcf" value="mpileup.AD.vcf" />
325 <param name="method" value="multiallelic" />
326 <param name="output_type" value="v" />
327 <section name="sec_consensus_variant_calling">
328 <conditional name="variant_calling">
329 <conditional name="genotypes">
330 <conditional name="targets">
331 <param name="targets_src" value="targets_file"/>
332 <param name="targets_file" value="targets_file.tab"/>
333 </conditional>
334 </conditional>
335 </conditional>
336 </section>
337 <output name="output_file">
338 <assert_contents>
339 <has_text text="--targets-file" />
340 <not_has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" />
341 </assert_contents>
342 </output>
343 </test>
315 </tests> 344 </tests>
316 <help><![CDATA[ 345 <help><![CDATA[
317 ================================== 346 ==================================
318 bcftools @EXECUTABLE@ 347 bcftools @EXECUTABLE@
319 ================================== 348 ==================================