comparison bcftools_roh.xml @ 16:6a636d58dfc2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49

15:78cd8b69da4c

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

    --buffer-size "${section.buffer_size},${section.buffer_overlap}"
  #else:
    --buffer-size "${section.buffer_size}"
  #end if
#end if

## HMM section
#set $section = $sec_hmm
#if $section.hw_to_az:
  --hw-to-az "${section.hw_to_az}"

            <param name="buffer_overlap" type="integer" min="0" label="Sliding Buffer Overlap" optional="True">
                <help>
The number of overlapping sites for the sliding buffer. The default overlap is set to roughly 1% of the buffer size. 
                </help>
            </param>
        </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" />

                    <not_has_text text="ST"/>
                    <has_text_matching expression="RG\tsample\t1"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================

16:6a636d58dfc2

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>HMM model for detecting runs of homo/autozygosity</description>
    <macros>
        <token name="@EXECUTABLE@">roh</token>
        <import>macros.xml</import>
    </macros>

    --buffer-size "${section.buffer_size},${section.buffer_overlap}"
  #else:
    --buffer-size "${section.buffer_size}"
  #end if
#end if
$section.ignore_homref
$section.include_noalt

## HMM section
#set $section = $sec_hmm
#if $section.hw_to_az:
  --hw-to-az "${section.hw_to_az}"

            <param name="buffer_overlap" type="integer" min="0" label="Sliding Buffer Overlap" optional="True">
                <help>
The number of overlapping sites for the sliding buffer. The default overlap is set to roughly 1% of the buffer size. 
                </help>
            </param>
            <param argument="--ignore-homref" type="boolean" truevalue="--ignore-homref" falsevalue="" checked="false" label="Ignore homo-ref" help="skip hom-ref genotypes (0/0)" />
            <param argument="--include-noalt" type="boolean" truevalue="--include-noalt" falsevalue="" checked="false" label="Include sites with no ALT allele" help="Ignored by default" />
        </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" />

                    <not_has_text text="ST"/>
                    <has_text_matching expression="RG\tsample\t1"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test ignore homref and include noalt-->
        <test>
            <param name="input_file" ftype="vcf" value="roh.vcf" />
            <param name="AF_dflt" value="0.4" />
            <param name="GTs_only" value="30" />
            <param name="output_type" value="r" />
            <param name="ignore_homref" value="true"/>
            <param name="include_noalt" value="true"/>
            <output name="output_file">
                <assert_contents>
                    <not_has_text text="ST"/>
                    <has_text_matching expression="RG\tsample\t1"/>
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--ignore-homref" />
                <has_text text="--include-noalt" />
            </assert_command>
        </test>
        <!-- Test region overlap-->
        <test>
            <param name="input_file" ftype="vcf" value="roh.vcf" />
            <section name="sec_general">
                <param name="AF_dflt" value="0.4" />
                <param name="GTs_only" value="30" />
            </section>
            <section name="sec_restrict">
                <param name="regions_overlap" value="1"/>
            </section>
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="ST\tsample\t1"/>
                    <has_text_matching expression="RG\tsample\t1"/>
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--regions-overlap" />
            </assert_command>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================