comparison beagle.xml @ 1:d0a6954d0a0a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8

0:117d42db0a30

    </macros>
    <expand macro='edam_ontology' />
    <expand macro='requirements' />
    <command detect_errors='exit_code'><![CDATA[
        #set out_prefix='out'
        #if $optional_inputs.ref.ext == 'bref3'
            ln -s '${optional_inputs.ref}' ref.bref3 &&
        #end if
        beagle
        gt='${gt}'
        #if $optional_inputs.ref and $optional_inputs.ref.ext == 'bref3'
            ref=ref.bref3
        #else if $optional_inputs.ref
            ref='${optional_inputs.ref}'
        #end if
        #if $optional_inputs.map
            map='${optional_inputs.map}'
        #end if
        #if $chrom

        </data>
    </outputs>
    <tests>
        <!-- Test default values -->
        <test expect_num_outputs="2">
            <param name="gt" value="test.vcf.gz"/>
            <param name="chrom" value="22:100-"/>
            <param name="ne" value="1000000"/>
            <param name="window" value="40.0"/>
            <param name="overlap" value="2.0"/>
            <param name="err" value="0.02"/>

                <param name="burnin" value="3"/>
                <param name="iterations" value="12"/>
                <param name="phase_states" value="280"/>
            </section>
            <output name="vcf_file" file="test_output.vcf" ftype="vcf" lines_diff="3"/>
            <output name="log_file" file="test_output.log" ftype="txt" lines_diff="16"/>
        </test>
        <!-- Test plink file-->
        <test expect_num_outputs="2">
            <param name="gt" value="test.vcf.gz"/>
            <param name="ne" value="1000000"/>
            <param name="window" value="30.0"/>
            <param name="overlap" value="3.0"/>
            <param name="output_log" value="true"/>
            <section name="optional_inputs">

                </assert_contents>
            </output>
            <output name="log_file" ftype="txt">
                <assert_contents>
                    <has_text text="Reference markers:                  223"/>
                    <has_size value="1586" delta="10"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test ref VCF input -->
        <test expect_num_outputs="2">
            <param name="gt" value="target.vcf.gz"/>
            <param name="ne" value="1000000"/>
            <param name="window" value="40.0"/>
            <param name="overlap" value="2.0"/>
            <param name="output_log" value="true"/>
            <section name="optional_inputs">
                <param name="ref" value="ref.vcf.gz"/>
            </section>
            <section name="imputation_parameters">
                <param name="impute" value="true"/>
                <param name="imp_states" value="1600"/>
                <param name="imp_segment" value="6.0"/>

                </assert_contents>
            </output>
            <output name="log_file" ftype="txt">
                <assert_contents>
                    <has_text text="Reference markers:                  223"/>
                    <has_size value="1801" delta="10"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test ref bref3 input -->
        <test expect_num_outputs="1">
            <param name="gt" value="target.vcf.gz"/>
            <param name="ne" value="1000000"/>
            <param name="window" value="40.0"/>
            <param name="overlap" value="2.0"/>
            <section name="optional_inputs">
                <param name="ref" value="ref.bref3"/>
            </section>
            <section name="imputation_parameters">
                <param name="impute" value="true"/>
                <param name="imp_states" value="1600"/>
                <param name="imp_segment" value="6.0"/>

.. class:: infomark

**HapMap genetic maps**

HapMap genetic maps in PLINK format for GRCh36, GRCh37, and GRCh38 are available 
in `this link <http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/>`_

----

.. class:: infomark

1:d0a6954d0a0a

    </macros>
    <expand macro='edam_ontology' />
    <expand macro='requirements' />
    <command detect_errors='exit_code'><![CDATA[
        #set out_prefix='out'
        #if $optional_inputs.ref
            ln -s '${optional_inputs.ref}' ref.$optional_inputs.ref.ext &&
        #end if

        beagle
        gt='${gt}'
        #if $optional_inputs.ref
            ref=ref.$optional_inputs.ref.ext
        #end if
        #if $optional_inputs.map
            map='${optional_inputs.map}'
        #end if
        #if $chrom

        </data>
    </outputs>
    <tests>
        <!-- Test default values -->
        <test expect_num_outputs="2">
            <param name="gt" value="test.vcf.gz" ftype="vcf"/>
            <param name="chrom" value="22:100-"/>
            <param name="ne" value="1000000"/>
            <param name="window" value="40.0"/>
            <param name="overlap" value="2.0"/>
            <param name="err" value="0.02"/>

                <param name="burnin" value="3"/>
                <param name="iterations" value="12"/>
                <param name="phase_states" value="280"/>
            </section>
            <output name="vcf_file" file="test_output.vcf" ftype="vcf" lines_diff="3"/>
            <output name="log_file" file="test_output.log" ftype="txt" lines_diff="16">
                <assert_contents>
                    <has_text text="WARNING" negate="true"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test plink file-->
        <test expect_num_outputs="2">
            <param name="gt" value="test.vcf.gz" ftype="vcf"/>
            <param name="ne" value="1000000"/>
            <param name="window" value="30.0"/>
            <param name="overlap" value="3.0"/>
            <param name="output_log" value="true"/>
            <section name="optional_inputs">

                </assert_contents>
            </output>
            <output name="log_file" ftype="txt">
                <assert_contents>
                    <has_text text="Reference markers:                  223"/>
                    <has_size value="1586" delta="100"/>
                    <has_text text="WARNING" negate="true"/>
                    <has_text_matching expression="beagle.*jar finished"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test ref VCF input -->
        <test expect_num_outputs="2">
            <param name="gt" value="target.vcf.gz" ftype="vcf"/>
            <param name="ne" value="1000000"/>
            <param name="window" value="40.0"/>
            <param name="overlap" value="2.0"/>
            <param name="output_log" value="true"/>
            <section name="optional_inputs">
                <param name="ref" value="ref.vcf.gz" ftype="vcf"/>
            </section>
            <section name="imputation_parameters">
                <param name="impute" value="true"/>
                <param name="imp_states" value="1600"/>
                <param name="imp_segment" value="6.0"/>

                </assert_contents>
            </output>
            <output name="log_file" ftype="txt">
                <assert_contents>
                    <has_text text="Reference markers:                  223"/>
                    <has_size value="1600" delta="100"/>
                    <has_text text="WARNING" negate="true"/>
                    <has_text_matching expression="beagle.*jar finished"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test ref bref3 input -->
        <test expect_num_outputs="1">
            <param name="gt" value="target.vcf.gz" ftype="vcf"/>
            <param name="ne" value="1000000"/>
            <param name="window" value="40.0"/>
            <param name="overlap" value="2.0"/>
            <section name="optional_inputs">
                <param name="ref" value="ref.bref3" ftype="bref3"/>
            </section>
            <section name="imputation_parameters">
                <param name="impute" value="true"/>
                <param name="imp_states" value="1600"/>
                <param name="imp_segment" value="6.0"/>

.. class:: infomark

**HapMap genetic maps**

HapMap genetic maps in PLINK format for GRCh36, GRCh37, and GRCh38 are available 
in `this links <https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/>`_

----

.. class:: infomark