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comparison bcftools_call.xml @ 9:cb30a39055d0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 13:17:26 -0400
parents 0fba2c15b40d
children 5801eff9ac7e
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8:0fba2c15b40d 9:cb30a39055d0
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@+galaxy1">
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">
110 > '$output_file' 110 > '$output_file'
111 ]]></command> 111 ]]></command>
112 <inputs> 112 <inputs>
113 <expand macro="macro_input" /> 113 <expand macro="macro_input" />
114 <section name="sec_restrict" expanded="false" title="Restrict to"> 114 <section name="sec_restrict" expanded="false" title="Restrict to">
115 <expand macro="macro_regions" /> 115 <expand macro="macro_restrict" />
116 <expand macro="macro_samples" /> 116 <expand macro="macro_samples" />
117 </section> 117 </section>
118 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options"> 118 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
119 <conditional name="variant_calling"> 119 <conditional name="variant_calling">
120 <param name="method" type="select" label="Calling method"> 120 <param name="method" type="select" label="Calling method">
127 <option value="none">Do not constrain</option> 127 <option value="none">Do not constrain</option>
128 <option value="alleles">alleles - call genotypes given alleles</option> 128 <option value="alleles">alleles - call genotypes given alleles</option>
129 <option value="trio">trio - call genotypes given the father-mother-child constraint</option> 129 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
130 </param> 130 </param>
131 <when value="none"> 131 <when value="none">
132 <expand macro="macro_targets" /> 132 <expand macro="macro_restrict" type="target" label_type="Target" />
133 </when> 133 </when>
134 <when value="alleles"> 134 <when value="alleles">
135 <expand macro="macro_targets_file"/> 135 <expand macro="macro_restrictions_file" type="target" label_type="Target" />
136 <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" /> 136 <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" />
137 </when> 137 </when>
138 <when value="trio"> 138 <when value="trio">
139 <expand macro="macro_targets" /> 139 <expand macro="macro_restrict" type="target" label_type="Target" />
140 <expand macro="macro_novel_rate" /> 140 <expand macro="macro_novel_rate" />
141 </when> 141 </when>
142 </conditional> 142 </conditional>
143 <param name="prior_freqs" argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies"> 143 <param name="prior_freqs" argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
144 <help> 144 <help>
163 <when value="none" /> 163 <when value="none" />
164 <when value="trio"> 164 <when value="trio">
165 <expand macro="macro_novel_rate" /> 165 <expand macro="macro_novel_rate" />
166 </when> 166 </when>
167 </conditional> 167 </conditional>
168 <expand macro="macro_targets" /> 168 <expand macro="macro_restrict" type="target" label_type="Target" />
169 <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" /> 169 <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" />
170 </when> 170 </when>
171 </conditional> 171 </conditional>
172 </section> 172 </section>
173 <section name="sec_file_format" expanded="false" title="File format Options"> 173 <section name="sec_file_format" expanded="false" title="File format Options">
177 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option> 177 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
178 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option> 178 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
179 <option value="1">1 - Treat all samples as haploid</option> 179 <option value="1">1 - Treat all samples as haploid</option>
180 </param> 180 </param>
181 <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" /> 181 <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" />
182 <expand macro="macro_regions" /> 182 <expand macro="macro_restrict" />
183 <expand macro="macro_samples" /> 183 <expand macro="macro_samples" />
184 </section> 184 </section>
185 <section name="sec_input_output" expanded="false" title="Input/output Options"> 185 <section name="sec_input_output" expanded="false" title="Input/output Options">
186 <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" /> 186 <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" />
187 <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample" 187 <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"