comparison bcftools_roh.xml @ 2:6ed9d03452ad draft

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

1:40d8186eb3bb

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
    <description>HMM model for detecting runs of autozygosity</description>
    <macros>
        <token name="@EXECUTABLE@">roh</token>
        <import>macros.xml</import>
    </macros>

            <param name="skip_indels" type="boolean" truevalue="--skip-indels" falsevalue="" label="Skip Indels" help="Skip indels as their genotypes are enriched for errors" />
            <param name="genetic_map" type="data" format="data" label="Genetic Map" optional="True" help="Genetic map in IMPUTE2 format, single file or mask, where string &quot;{CHROM}&quot; is replaced with chromosome name" />
            <param name="rec_rate" type="float" label="Rec Rate" optional="True" help="Constant recombination rate per bp" />
        </section>
        <section name="sec_hmm" expanded="true" title="HMM Options">
            <param name="hw_to_az" type="float" label="Hw To Az" default="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" />
            <param name="az_to_hw" type="float" label="Az To Hw" default="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" />
            <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" />
        </section>
    </inputs>
    <outputs>
        <data name="output_file" format="tabular"/>

2:6ed9d03452ad

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
    <description>HMM model for detecting runs of autozygosity</description>
    <macros>
        <token name="@EXECUTABLE@">roh</token>
        <import>macros.xml</import>
    </macros>

            <param name="skip_indels" type="boolean" truevalue="--skip-indels" falsevalue="" label="Skip Indels" help="Skip indels as their genotypes are enriched for errors" />
            <param name="genetic_map" type="data" format="data" label="Genetic Map" optional="True" help="Genetic map in IMPUTE2 format, single file or mask, where string &quot;{CHROM}&quot; is replaced with chromosome name" />
            <param name="rec_rate" type="float" label="Rec Rate" optional="True" help="Constant recombination rate per bp" />
        </section>
        <section name="sec_hmm" expanded="true" title="HMM Options">
            <param name="hw_to_az" type="float" label="Hw To Az" value="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" />
            <param name="az_to_hw" type="float" label="Az To Hw" value="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" />
            <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" />
        </section>
    </inputs>
    <outputs>
        <data name="output_file" format="tabular"/>