comparison bcftools_call.xml @ 3:5337db17a5f7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6

2:99dff9c8b2f3

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
    <description>SNP/indel variant calling from VCF/BCF</description>
    <macros>
        <token name="@EXECUTABLE@">call</token>
        <import>macros.xml</import>
    </macros>

                            <expand macro="macro_targets_file"/>
                            <param name="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" />
                            <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
                        </when>
                    </conditional>
                    <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
                </when>
                <when value="consensus">

                            <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
                        </param>
                        <when value="none">
                        </when>
                        <when value="trio">
                            <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
                        </when>
                    </conditional>
                    <expand macro="macro_targets" />
                </when>
            </conditional>
            <param name="pval_threshold" type="float" label="Pval Threshold" default="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" />
            <param name="prior" type="float" label="Prior" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
        </section>
        <section name="sec_file_format" expanded="false" title="File format Options">
            <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true">
                <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option>
                <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>

3:5337db17a5f7

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
    <description>SNP/indel variant calling from VCF/BCF</description>
    <macros>
        <token name="@EXECUTABLE@">call</token>
        <import>macros.xml</import>
    </macros>

                            <expand macro="macro_targets_file"/>
                            <param name="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" />
                            <param name="novel_rate" type="float" label="Novel Rate" value="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
                        </when>
                    </conditional>
                    <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
                </when>
                <when value="consensus">

                            <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
                        </param>
                        <when value="none">
                        </when>
                        <when value="trio">
                            <param name="novel_rate" type="float" label="Novel Rate" value="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
                        </when>
                    </conditional>
                    <expand macro="macro_targets" />
                </when>
            </conditional>
            <param name="pval_threshold" type="float" label="Pval Threshold" value="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" />
            <param name="prior" type="float" label="Prior" value="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
        </section>
        <section name="sec_file_format" expanded="false" title="File format Options">
            <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true">
                <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option>
                <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>