view king.xml @ 1:1932808c6fab draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"

<?xml version="1.0" encoding="utf-8"?>
<tool id="king" name="KING" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Kinship-based INference for GWAS</description>
    <macros>
        <token name="@TOOL_VERSION@">2.2.7</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">king</requirement>
        <requirement type="package" version="1.8.5">r-kinship2</requirement>
        <requirement type="package" version="1.3.0">r-igraph</requirement>
        <requirement type="package" version="1.7_9">r-e1071</requirement>
    </requirements>
    <version_command>
        king | head -1 | cut -d' ' -f 2
    </version_command>
    <command detect_errors="exit_code"><![CDATA[
    ln -s '$genotype' input.bed &&

    #if $opt_int.family:
        ln -s '$opt_int.family' input.fam &&
    #end if
    #if $opt_int.map:
        ln -s '$opt_int.map' input.bim &&
    #end if
    #if $gen_rsk.model:
        ln -s '$gen_rsk.model' input.model &&
    #end if
    ## General Input
    king -b input.bed
    ## Close Relative Inference
    $close_rel_i.related
    $close_rel_i.duplicate
    ## Pairwise Relatedness Inference
    $pair_rel_i.kinship
    $pair_rel_i.ibdseg
    $pair_rel_i.ibs
    $pair_rel_i.homog
    ## Inference Parameter
    #if str($inf_param.degree):
        --degree $inf_param.degree
    #end if
    #if str($inf_param.seglength):
        --seglength $inf_param.seglength
    #end if
    ## Relationship Application
    $rel_app.unrelated
    $rel_app.cluster
    $rel_app.build
    ## QC Report
    #if str($qc_rep.callrateN):
        --callrateN $callrateN
    #end if
    #if str($qc_rep.callrateM):
        --callrateM $callrateM
    #end if
    ## Population Structure
    $pop_str.pca
    $pop_str.mds
    ## Structure Parameter
    #if str($str_par.pcs)
        --pcs $str_par.pcs
    #end if
    #if str($str_par.projection)
        --projection $str_par.projection
    #end if
    ## Disease Assosciation
    $dis_ass.tdt
    ## Quantitiative Trait Association
    $qnt_trt.mtscore
    ## Association Model
    #if str($ass_mod.trait)
        --trait $ass_mod.trait
    #end if
    #if str($ass_mod.covariate)
        --covariate $ass_mod.covariate
    #end if
    ## Association parameter
    $ass_par.invnorm
    #if str($ass_par.maxP)
        --maxP $ass_par.maxP
    #end if
    ## Genetic Risk Score
    $gen_rsk.risk
    #if $gen_rsk.model:
        --model input.model
    #end if
    #if str($gen_rsk.prevalence)
    --prevalence $gen_rsk.prevalence
    #end if
    $gen_rsk.noflip
    ## Computing parameter
    --cpus "\${GALAXY_SLOTS:-4}"
    ## Optional Input
    #if $opt_int.family
        --fam input.fam
    #end if
    #if $opt_int.map
        --bim input.bim
    #end if
    #if $opt_int.sexchr
        --sexchr $opt_int.sexchr
    #end if
    ## Output
    $opt_par.rplot
    $opt_par.pngplot
    $opt_par.plink
    > '$kingoutlog'
    ]]></command>
    <inputs>
        <param name="genotype" type="data" format="pbed" label="Binary Genotype File" help="Generated by PLINK" />
        <!-- Beginning of the optional paramters -->
        <section name="close_rel_i" title="Close Relative Inference" >
            <param argument="--related" type="boolean" truevalue="--related" falsevalue=""
                   label="Relationship Inference"
                   help="Implements the fastest and integrated relationship inference." />
            <param argument="--duplicate" type="boolean" truevalue="--duplicate" falsevalue=""
                   label="Duplicate Analysis"
                   help="Implements the fastest (and accurate) algorithm to identify duplicates or MZ twins" />
        </section>
        <!-- Despite many of the below parameters being grouped together, they can all
             surprisingly be used independently of one another, i.e. no mutual exclusivity that I can see -->
        <section name="pair_rel_i" title="Pairwise Relative Inference" >
            <param argument="--kinship" type="boolean" truevalue="--kinship" falsevalue=""
                   label="Kinship Inference"
                   help="Estimates pair-wise kinship coefficients" />
            <param argument="--ibdseg" type="boolean" truevalue="--ibdseg" falsevalue=""
                   label="IBD Segment Analysis"
                   help="IBD segment analysis determines all IBD (IBD1 and IBD2) segments shared between relatives" />
            <param argument="--ibs" type="boolean" truevalue="--ibs" falsevalue=""
                   label="IBS Summary Statistics"
                   help="Counts and average of IBS" />
            <param argument="--homog" type="boolean" truevalue="--homog" falsevalue=""
                   label="Homogeneous Population"
                   help="Estimates pair-wise kinship coefficients assuming a homogeneous population." />
        </section>
        <section name="inf_param" title="Inference Parameter" >
            <param argument="--degree" type="integer" min="0" optional="true"
                   label="Degrees of relatedness"
                   help="Filters relative pairs based on kinship coefficients." />
            <param argument="--seglength" type="integer" min="1" optional="true"
                   label="Minimum IBD segments"
                   help="specifies the minimum length of IDB segments that are considered towards the relationship inference" />
        </section>
        <section name="rel_app" title="Relationship Application" >
            <param argument="--unrelated" type="boolean" truevalue="--unrelated" falsevalue=""
                   label="Unrelated Option"
                   help="Extract a list of unrelated individuals." />
            <param argument="--cluster" type="boolean" truevalue="--cluster" falsevalue=""
                   label="Cluster Parameter"
                   help="Clusters relatives into families by generating an updateid file." />
            <param argument="--build" type="boolean" truevalue="--build" falsevalue=""
                   label="Reconstruct Pedigree"
                   help="Reconstructs pedigrees using SNP data" />
        </section>
        <section name="qc_rep" title="QC Report" >
            <param argument="--callrateN" type="integer" min="1" optional="true"
                   label="Set the N callrate" />
            <param argument="--callrateM" type="integer" min="1" optional="true"
                   label="Set the M callrate" />
        </section>
        <section name="pop_str" title="Population Structure" >
            <param argument="--pca" type="boolean" truevalue="--pca" falsevalue=""
                   label="Add PCA as dimension reduction algorithm" />
            <param argument="--mds" type="boolean" truevalue="--mds" falsevalue=""
                   label="Add MDS as dimension reduction algorithm" />
        </section>
        <section name="str_par" title="Structure Parameter" >
            <!-- Ye, all options can be selected here, apparently... -->
            <param argument="--pcs" type="integer" min="1" optional="true"
                   label="Number of Principal Components to use"
                   help="allow the specification of the number of PCs with a default value of 10." />
            <param argument="--projection" type="integer" min="0" optional="true"
                   label="Projection N"
                   help="Includes the first N samples of a subset." />
        </section>
        <section name="dis_ass" title="Disease Association" >
            <param argument="--tdt" type="boolean" truevalue="--tdt" falsevalue=""
                   label="Transmission/Disequilibrium Test"
                   help="implements the well-known Transmission/Disequilibrium Test for family data that consist of parent-affected child trios." />
        </section>
        <section name="qnt_trt" title="Quantitative Trait Association" >
            <param argument="--mtscore" type="boolean" truevalue="--mtscore" falsevalue=""
                   label="Score Test between SNP and quantitative trait"
                   help="Only association results with P value less than 5E-8 are printed out, including both cis- and trans- effect associations. "/>
        </section>
        <section name="ass_mod" title="Association Model" >
            <param argument="--trait" type="text" optional="true"
                   label="Trait names"
                   help="Specifies the trait names to be analyzed in the association analysis." />
            <param argument="--covariate" type="text" optional="true"
                   label="Covariate names"
                   help="Specifies the covariate names to be adjusted in the association analysis" />
        </section>
        <section name="ass_par" title="Association Parameter" >
            <param argument="--invnorm" type="boolean" truevalue="--invnorm" falsevalue=""
                   label="Normal Transformation"
                   help="Carries out inverse normal transformation for quantitative traits prior to association analysis."/>
            <param argument="--maxP" type="float" min="0" optional="true"
                   label="maximum P values"
                   help="specifies the maximum P values to print out in the output files."/>
        </section>
        <section name="gen_rsk" title="Genetic Risk Score" >
            <param argument="--risk" type="boolean" truevalue="--risk" falsevalue=""
                   label="Predict Disease Risk"
                   help="predicts disease risks for each individual according to the GRS risk model" />
            <param name="model" type="data" format="txt,tabular" label="GRS Risk Model file" optional="true" />
            <param argument="--prevalence" type="float" min="0" optional="true"
                   label="Disease prevalence" />
            <param argument="--noflip" type="boolean" truevalue="--noflip" falsevalue=""
                   label="No Flip"
                   help="If strands of genotype data are already consistent with model, enable this." />
        </section>
        <section name="opt_int" title="Optional Input" >
            <param name="family" type="data" format="lped,txt" label="Family File" optional="true" />
            <param name="map" type="data" format="tabular" label="Map File" optional="true" />
            <param argument="--sexchr" type="integer" min="0" optional="true"
                   label="Pair number of the Sex Chromosome."
                   help="specifies the pair number of the sex chromosome, which should be userful for non-human species. The default sex chromosome is 23." />
        </section>
        <section name="opt_par" title="Optional Parameter" >
            <param argument="--rplot" type="boolean" truevalue="--rplot" falsevalue=""
                   label="R Code and Plots"
                   help="Generates R code first and then calls R program to make plots in a PDF file." />
            <param argument="--pngplot" type="boolean" truevalue="--pngplot" falsevalue=""
                   label="R Code and Plots in PNG format"
                   help="Generates R code first and then calls R program to make plots in a PNG file for certain applications." />
            <param argument="--plink" type="boolean" truevalue="--plink" falsevalue=""
                   label="Output data in PLINK format" />
        </section>
        <param name="use_log" type="boolean" checked="false"
               label="Output a Log?" />
    </inputs>
    <outputs>
        <data name="kingoutlog" format="txt" label="${tool.name} on ${on_string} : Log" >
            <filter>use_log == True</filter>
        </data>
        <collection name="kingoutput_txt" type="list" label="${tool.name} on ${on_string}: Metrics">
            <discover_datasets pattern="king(?P&lt;name&gt;.+)\.txt" format="txt"  />
            <discover_datasets pattern="king\.(?P&lt;name&gt;.+)" format="txt"  />
            <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.plink" format="plink" />
            <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.R" format="txt" />
        </collection>
        <collection name="kingoutput_log" type="list" label="${tool.name} on ${on_string}: Metrics Logs" >
            <filter>use_log == True</filter>
            <discover_datasets pattern="king(?P&lt;name&gt;.+)\.log" format="txt" />
            <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.Rout" format="txt" />
        </collection>
        <collection name="kingoutput_pdf" type="list" label="${tool.name} on ${on_string}: Plots">
            <filter>opt_par["rplot"] or opt_par["pngplot"]</filter>
            <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.pdf" format="pdf" />
            <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.png" format="png" />
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="close_rel_i" >
                <param name="related" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is"/>
                    <has_text text="Information of these chromosomal segments can be found in file kingallsegs.txt" />
                    <has_text text="--related" />
                    <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="close_rel_i" >
                <param name="related" value="true" />
            </section>
            <section name="inf_param" >
                <param name="degree" value="2" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is"/>
                    <has_text text="Information of these chromosomal segments can be found in file kingallsegs.txt" />
                    <has_text text="--related" />
                    <has_text text="--degree 2" />
                    <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="close_rel_i" >
                <param name="related" value="true" />
            </section>
            <section name="inf_param" >
                <param name="degree" value="2" />
            </section>
            <section name="opt_par" >
                <param name="rplot" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/>
                    <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
                    <has_text text="--related" />
                    <has_text text="--degree 2" />
                    <has_text text="--rplot" />
                    <has_text text="(with 6000 SNPs): 8 pairs of relatives are detected (with kinship > 0.0625)" />
                    <has_text text="Relationship summary (total relatives: 0 by pedigree, 6 by inference)" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="close_rel_i" >
                <param name="duplicate" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/>
                    <has_text text="--duplicate" />
                    <has_text text="No duplicates are found with heterozygote concordance rate > 80%." />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="pair_rel_i" >
                <param name="kinship" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/>
                    <has_text text="--kinship" />
                    <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="close_rel_i" >
                <param name="related" value="true" />
            </section>
            <section name="str_par" >
                <param name="projection" value="100000" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/>
                    <has_text text="--related" />
                    <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
                    <has_text text="PLINK pedigrees loaded: 332 samples" />
                    <has_text text="PLINK maps loaded: 6000 SNPs" />
                    <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="pair_rel_i" >
                <param name="ibdseg" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="--ibdseg" />
                    <has_text text="Sample pairs without any long IBD segments (>10Mb) are excluded." />
                    <has_text text="IBD segments saved in a gzipped file king.segments.gz" />
                    <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="pair_rel_i" >
                <param name="ibdseg" value="true" />
            </section>
            <section name="inf_param" >
                <param name="degree" value="3" />
            </section>
            <section name="opt_par" >
                <param name="rplot" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="--ibdseg" />
                    <has_text text="--rplot" />
                    <has_text text="--degree 3" />
                    <has_text text="Summary statistics of IBD segments for individual pairs saved in file king.seg" />
                    <has_text text="Genotype data consist of 6000 autosome SNPs" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="pair_rel_i" >
                <param name="ibs" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." />
                    <has_text text="Within-family IBS data saved in file king.ibs" />
                    <has_text text="--ibs" />
                    <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
                    <has_text text="Information of these chromosomal segments can be found in file kingallsegs.txt" />
                    <has_text text="Between-family IBS data saved in file king.ibs0" />
                    <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="pair_rel_i" >
                <param name="homog" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="Autosome genotypes stored in 375 words for each of 332 individuals." />
                    <has_text text="--homo" />
                    <has_text text="Within-family kinship data saved in file king.kin" />
                    <has_text text="Genotype data consist of 6000 autosome SNPs" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="rel_app" >
                <param name="unrelated" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="--unrelated" />
                    <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
                    <has_text text="Y028,Y117" />
                    <has_text text="An alternative list of 114 to-be-removed individuals saved in file kingunrelated_toberemoved.txt" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="rel_app" >
                <param name="unrelated" value="true" />
            </section>
            <section name="inf_param" >
                <param name="degree" value="2" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog" >
                <assert_contents>
                    <has_text text="--unrelated" />
                    <has_text text="--degree 2" />
                    <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." />
                    <has_text text="An alternative list of 114 to-be-removed individuals saved in file kingunrelated_toberemoved.txt" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="rel_app" >
                <param name="build" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog" >
                <assert_contents>
                    <has_text text="--build" />
                    <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." />
                    <has_text text="Update-ID information is saved in file kingupdateids.txt" />
                    <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="rel_app" >
                <param name="build" value="true" />
            </section>
            <section name="inf_param" >
                <param name="degree" value="2" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="--build" />
                    <has_text text="--degree 2" />
                    <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
                    <has_text text="Update-parent information is saved in file kingupdateparents.txt" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="rel_app" >
                <param name="cluster" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text text="--cluster" />
                    <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
                    <has_text text="Pair-wise relatedness in newly clustered families saved in kingcluster.kin." />
                </assert_contents>
            </output>
        </test>
        <test> <!-- risk prediction -->
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="gen_rsk">
                <param name="model" ftype="txt" value="test.model" />
                <param name="risk" value="true"/>
                <param name="prevalence" value="0.004"/>
                <param name="noflip" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog" >
                <assert_contents>
                    <has_text text="rs2602970    11     T     A   0.265   0.403     C     T   0.474   SWITCHED" />
                    <has_text text="rs1161312    17     C     T   0.459   0.295     G     A   0.408    FLIPPED" />
                </assert_contents>
            </output>
            <output_collection name="kingoutput_txt" count="1">
                <element name="grs" >
                    <assert_contents>
                        <has_text text="13292         NA07014   1.000   1.000   4.917   3.243  0.0006    0.9927" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="3" > <!-- association mapping 1 -->
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="dis_ass">
                <param name="tdt" value="true" />
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog" >
                <assert_contents>
                    <has_text text="There are no parent-affected-offspring trios in the data." />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3"> <!-- association mapping 2 -->
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="ass_mod">
                <param name="covariate" value="," />
            </section>
            <section name="qnt_trt" >
                <param name="mtscore" value="false"/>
            </section>
            <section name="ass_par">
                <param name="invnorm" value="true" />
                <param name="maxP" value="5e-8"/>
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog" >
                <assert_contents>
                    <has_text_matching expression="Inference\s+0\s+1\s+1\s+0" />
                </assert_contents>
            </output>
            <output_collection name="kingoutput_txt" count="3" >
                <element name="allsegs" >
                    <assert_contents>
                        <has_text_matching expression="1\s+1\s+51\.\d+\s+95\.\d+\s+44\.\d+\s+294\s+rs7534689\s+rs1858111" />
                    </assert_contents>
                </element>
                <element name="kin0" >
                    <assert_contents>
                        <has_text_matching expression="FID1\s+ID1\s+FID2\s+ID2\s+N_SNP\s+HetHet\s+IBS0\s+HetConc\s+HomIBS0\s+Kinship\s+IBD1Seg\s+IBD2Seg\s+PropIBD\s+InfType" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="4" > <!-- ancestry inferrence -->
            <param name="genotype" value="new.6000.bed"/>
            <section name="opt_int" >
                <param name="family" value="new.6000.fam"/>
                <param name="map" value="new.6000.bim"/>
            </section>
            <section name="pop_str">
                <param name="pca" value="true" />
            </section>
            <section name="str_par" >
                <param name="projection" value="1"/>
            </section>
            <section name="opt_par">
                <param name="rplot" value="true"/>
                <param name="pngplot" value="true"/>
            </section>
            <param name="use_log" value="true" />
            <output name="kingoutlog">
                <assert_contents>
                    <has_text_matching expression="10\s+eigenvalues:\s+581\.\d+\s+114\.\d+\s+112\.\d+\s+111\.\d+\s+109\.\d+\s+109\.\d+\s+108\.\d+\s+108\.\d+\s+107\.\d+\s+107\.\d+" />
                </assert_contents>
            </output>
            <output_collection name="kingoutput_txt" count="3" >
                <element name="pc">
                    <assert_contents>
                        <has_text_matching expression="Y117\s+NA19239\s+0\s+0\s+1\s+1\s+.*" />
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="kingoutput_log" count="2" />
            <output_collection name="kingoutput_pdf" count="1" >
                <element name="pcplot" value="king_pcplot.png" compare="sim_size" delta="2500" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[

    `KING <http://people.virginia.edu/~wc9c/KING/>`_ is a toolset that makes use of
    high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a
    sequencing project. Applications of KING include family relationship inference and
    pedigree error checking, quality control, population substructure identification,
    forensics, gene mapping, etc.

    ]]>
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btq559</citation>
    </citations>
</tool>