Mercurial > repos > iuc > bcftools_call

comparison bcftools_call.xml @ 21:1001172b5089 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
author iuc
date Tue, 16 Jul 2024 17:07:11 +0000
parents 22637b1a55bf
children bf06b66ab5c2
comparison
equal deleted inserted replaced
20:f0d44631365f 21:1001172b5089
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 </when> 139 </when>
140 <when value="alleles"> 140 <when value="alleles">
141 <expand macro="macro_restrictions_file" type="target" label_type="Target" /> 141 <expand macro="macro_restrictions_file" type="target" label_type="Target" />
142 <param name="insert_missed" argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" /> 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" />
143 </when> 143 </when>
144 <when value="trio"> 144 <when value="trio">
145 <expand macro="macro_restrict" type="target" label_type="Target" /> 145 <expand macro="macro_restrict" type="target" label_type="Target" />
146 <expand macro="macro_novel_rate" /> 146 <expand macro="macro_novel_rate" />
147 </when> 147 </when>
148 </conditional> 148 </conditional>
149 <param name="prior_freqs" argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies"> 149 <param argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
150 <help> 150 <help>
151 <![CDATA[ 151 <![CDATA[
152 For example: --prior-freqs REF_AN,REF_AC 152 For example: --prior-freqs REF_AN,REF_AC
153 <br>if the input VCF has the following INFO tags: 153 <br>if the input VCF has the following INFO tags:
154 <br>##INFO=&lt;ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes"&gt; 154 <br>##INFO=&lt;ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes"&gt;
170 <when value="trio"> 170 <when value="trio">
171 <expand macro="macro_novel_rate" /> 171 <expand macro="macro_novel_rate" />
172 </when> 172 </when>
173 </conditional> 173 </conditional>
174 <expand macro="macro_restrict" type="target" label_type="Target" /> 174 <expand macro="macro_restrict" type="target" label_type="Target" />
175 <param name="pval_threshold" argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" /> 175 <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> 176 </when>
177 </conditional> 177 </conditional>
178 </section> 178 </section>
179 <section name="sec_file_format" expanded="false" title="File format Options"> 179 <section name="sec_file_format" expanded="false" title="File format Options">
180 <param argument="--ploidy" type="select" optional="true" label="Select predefined ploidy"> 180 <param argument="--ploidy" type="select" optional="true" label="Select predefined ploidy">
182 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option> 182 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>
183 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option> 183 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
184 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option> 184 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
185 <option value="1">1 - Treat all samples as haploid</option> 185 <option value="1">1 - Treat all samples as haploid</option>
186 </param> 186 </param>
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" /> 187 <param argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
188 <expand macro="macro_restrict" /> 188 <expand macro="macro_restrict" />
189 <expand macro="macro_samples" /> 189 <expand macro="macro_samples" />
190 </section> 190 </section>
191 <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)" /> 192 <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)" />
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" /> 193 <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" />
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" 194 <param argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"
195 help="Currently GQ and GP fields are supported" > 195 help="Currently GQ and GP fields are supported" >
196 <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>
197 </param> 197 </param>
198 <param name="keep_masked_ref" argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N" /> 198 <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" />
199 <param name="skip_variants" argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites"> 199 <param argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites">
200 <option value="indels">indels</option> 200 <option value="indels">indels</option>
201 <option value="snps">snps</option> 201 <option value="snps">snps</option>
202 </param> 202 </param>
203 <param name="variants_only" argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" /> 203 <param argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" />
204 <expand macro="macro_output_tags"> 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> 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> 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> 207 <option value="FORMAT/GP">FORMAT/GP: Phred-scaled genotype posterior probabilities</option>
208 </expand> 208 </expand>