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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit d64fadb1f41a602ea4fcec8f26ab18a4f92b8c90

<tool id="gemma" name="GEMMA Analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
    <description>Run association tests and kinship analysis with GEMMA</description>
    <macros>
        <token name="@TOOL_VERSION@">0.98.5</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">gemma</requirement>
    </requirements>

    <command detect_errors="aggressive"><![CDATA[

ln -s '$bed.extra_files_path'/*.bed input.bed &&
ln -s '$bed.extra_files_path'/*.bim input.bim &&
ln -s '$bed.extra_files_path'/*.fam input.fam &&

#if $lmm_inputs.analysis == "lmm"
    gemma -bfile input -k '$lmm_inputs.kinship' -lmm 1 -o gemmarun 2>&1;
    cp ./output/gemmarun.assoc.txt '$gemma_output';
    awk -F'\t' 'BEGIN {OFS="\t"} {print $1, $3, $3, $2, $4, $5, $6, $7, $8, $9, $10, $11, $12}' '$gemma_output' > '$gemma_output_int';
#elif $lmm_inputs.analysis == "gk"
    gemma -bfile input -gk 1 -o gemmarun 2>&1;
    cp ./output/gemmarun.cXX.txt '$gemma_output';
#else
    gemma -bfile input -lm 1 -o gemmarun 2>&1;
    cp ./output/gemmarun.assoc.txt '$gemma_output';
    awk -F'\t' 'BEGIN {OFS="\t"} {print $1, $3, $3, $2, $4, $5, $6, $7, $8, $9, $10, $11, $12}' '$gemma_output' > '$gemma_output_int';
#end if
]]> </command>
    <inputs>
        <param name="bed" type="data" format="pbed" label="Input PLINK dataset"/>
        <conditional name="lmm_inputs">
            <param name="analysis" type="select" label="Type of analysis to perform">
                <option value="lm">Linear Model (LM)</option>
                <option value="lmm">Linear Mixed Model (LMM)</option>
                <option value="gk">Kinship (Genetic Relationship Matrix)</option>
            </param>
            <when value="lmm">
                <param name="kinship" type="data" format="tsv,tabular" label="Kinship Matrix File" />
            </when>
            <when value="lm"></when>
            <when value="gk"></when>
        </conditional>
    </inputs>
    <outputs>
        <data name="gemma_output" format="tsv" label="GEMMA output file"/>
        <data name="gemma_output_int" format="interval" label="GEMMA output file interval">
            <filter>lmm_inputs['analysis'] != 'gk'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="lmm_inputs|analysis" value="lm" />
            <param name="bed" ftype="pbed" value="">
                <composite_data value="rgenetics.bim"/>
                <composite_data value="rgenetics.bed"/>
                <composite_data value="rgenetics.fam"/>
            </param>
            <output name="gemma_output" file="lm_output.tsv"/>
            <output name="gemma_output_int" file="lm_output.interval"/>
        </test>
        <test expect_num_outputs="1">
            <param name="lmm_inputs|analysis" value="gk" />
            <param name="bed" ftype="pbed" value="">
                <composite_data value="rgenetics.bim"/>
                <composite_data value="rgenetics.bed"/>
                <composite_data value="rgenetics.fam"/>
            </param>
            <output name="gemma_output" file="test_kinship_matrix.tsv"/>
        </test>
        <test expect_num_outputs="2">
            <param name="lmm_inputs|analysis" value="lmm" />
            <param name="bed" ftype="pbed" value="">
                <composite_data value="rgenetics.bim"/>
                <composite_data value="rgenetics.bed"/>
                <composite_data value="rgenetics.fam"/>
            </param>
            <param name="lmm_inputs|kinship" value="test_kinship_matrix.tsv" />
            <output name="gemma_output" file="lmm_output.tsv"/>
            <output name="gemma_output_int" file="lmm_output.interval"/>
        </test>
    </tests>
    <help>

This tool runs various GEMMA analyses. Choose from:
- LM: Linear Model for association testing.
- LMM: Linear Mixed Model for association testing with relatedness (requires a kinship matrix).
- GK: Kinship calculation (genetic relationship matrix).
    
Provide a PLINK binary dataset as input. For LMM, also provide a precomputed kinship matrix.
For lm/lmm analysis, the tool applies the Wald test.
    </help>
    <citations>
        <citation type="doi">10.1038/ng.2310</citation>
    </citations>
</tool>