comparison bcftools_call.xml @ 9:cb30a39055d0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5

8:0fba2c15b40d

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
    <description>SNP/indel variant calling from VCF/BCF</description>
    <macros>
        <token name="@EXECUTABLE@">call</token>
        <import>macros.xml</import>
        <xml name="macro_novel_rate">

> '$output_file'
    ]]></command>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_regions" />
            <expand macro="macro_samples" />
        </section>
        <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
            <conditional name="variant_calling">
                <param name="method" type="select" label="Calling method">

                            <option value="none">Do not constrain</option>
                            <option value="alleles">alleles - call genotypes given alleles</option>
                            <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
                        </param>
                        <when value="none">
                            <expand macro="macro_targets" />
                        </when>
                        <when value="alleles">
                            <expand macro="macro_targets_file"/>
                            <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" />
                        </when>
                        <when value="trio">
                            <expand macro="macro_targets" />
                            <expand macro="macro_novel_rate" />
                        </when>
                    </conditional>
                    <param name="prior_freqs" argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
                        <help>

                        <when value="none" />
                        <when value="trio">
                            <expand macro="macro_novel_rate" />
                        </when>
                    </conditional>
                    <expand macro="macro_targets" />
                    <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" />
                </when>
            </conditional>
        </section>
        <section name="sec_file_format" expanded="false" title="File format Options">

                <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
                <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
                <option value="1">1 - Treat all samples as haploid</option>
            </param>
            <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" />
            <expand macro="macro_regions" />
            <expand macro="macro_samples" />
        </section>
        <section name="sec_input_output" expanded="false" title="Input/output Options">
            <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" />
            <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"

9:cb30a39055d0

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
    <description>SNP/indel variant calling from VCF/BCF</description>
    <macros>
        <token name="@EXECUTABLE@">call</token>
        <import>macros.xml</import>
        <xml name="macro_novel_rate">

> '$output_file'
    ]]></command>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_restrict" />
            <expand macro="macro_samples" />
        </section>
        <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
            <conditional name="variant_calling">
                <param name="method" type="select" label="Calling method">

                            <option value="none">Do not constrain</option>
                            <option value="alleles">alleles - call genotypes given alleles</option>
                            <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
                        </param>
                        <when value="none">
                            <expand macro="macro_restrict" type="target" label_type="Target" />
                        </when>
                        <when value="alleles">
                            <expand macro="macro_restrictions_file" type="target" label_type="Target" />
                            <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" />
                        </when>
                        <when value="trio">
                            <expand macro="macro_restrict" type="target" label_type="Target" />
                            <expand macro="macro_novel_rate" />
                        </when>
                    </conditional>
                    <param name="prior_freqs" argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
                        <help>

                        <when value="none" />
                        <when value="trio">
                            <expand macro="macro_novel_rate" />
                        </when>
                    </conditional>
                    <expand macro="macro_restrict" type="target" label_type="Target" />
                    <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" />
                </when>
            </conditional>
        </section>
        <section name="sec_file_format" expanded="false" title="File format Options">

                <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
                <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
                <option value="1">1 - Treat all samples as haploid</option>
            </param>
            <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" />
            <expand macro="macro_restrict" />
            <expand macro="macro_samples" />
        </section>
        <section name="sec_input_output" expanded="false" title="Input/output Options">
            <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" />
            <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"