comparison bcftools_call.xml @ 25:3d17c458148a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 868f4386992de55d25da197660a43a913a09c8df

24:d6d682b69e65

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

                            <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 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 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 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">

                    <has_text text="bcftools_callCommand=call -m --prior 0.0011 --group-samples - " />
                    <has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
==================================
 bcftools @EXECUTABLE@
==================================

25:3d17c458148a

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
    <description>SNP/indel variant calling from VCF/BCF</description>
    <macros>
        <token name="@EXECUTABLE@">call</token>
        <import>macros.xml</import>
        <xml name="macro_novel_rate">

                            <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">
                                <expand macro="macro_invert_targets"/>
                            </expand>
                        </when>
                        <when value="alleles">
                            <expand macro="macro_restrictions_file" type="target" label_type="Target" />
                            <expand macro="macro_invert_targets"/>
                            <param 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_invert_targets"/>
                            </expand>
                            <expand macro="macro_novel_rate" />
                        </when>
                    </conditional>
                    <param 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">
                        <expand macro="macro_invert_targets" type="target" label_type="Target" />
                    </expand>
                    <param 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">

                    <has_text text="bcftools_callCommand=call -m --prior 0.0011 --group-samples - " />
                    <has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" />
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- Test targets-file option-->
            <param name="input_file" ftype="vcf" value="mpileup.AD.vcf" />
            <param name="method" value="multiallelic" />
            <param name="output_type" value="v" />
            <section name="sec_consensus_variant_calling">
                <conditional name="variant_calling">
                    <conditional name="genotypes">
                        <conditional name="targets">
                            <param name="targets_src" value="targets_file"/>
                            <param name="targets_file" value="targets_file.tab"/>
                        </conditional>
                    </conditional>
                </conditional>
            </section>
            <output name="output_file">
                <assert_contents>
                    <has_text text="--targets-file" />
                    <not_has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
==================================
 bcftools @EXECUTABLE@
==================================