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

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
author iuc
date Mon, 18 Apr 2022 18:04:56 +0000
parents ec2bc87ebd7b
children
line wrap: on
line diff
--- a/king.xml	Tue Nov 16 20:14:31 2021 +0000
+++ b/king.xml	Mon Apr 18 18:04:56 2022 +0000
@@ -2,82 +2,266 @@
 <tool id="king" name="KING" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Kinship-based INference for GWAS</description>
     <macros>
-        <token name="@TOOL_VERSION@">2.2.4</token>
+        <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="1.6.4">r-kinship2</requirement>
-        <requirement type="package" version="1.2.2">r-igraph</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 '$genotype' input.bed &&
-    ln -s '$family' input.fam &&
-    ln -s '$map' input.bim &&
 
-    king -b input.bed --fam input.fam --bim input.bim
-    $related
-    $duplicate
-    $kinship
-    $ibdseg
-    $ibs
-    $homog
-    #if str($degree):
-    --degree $degree
+    #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 $str_par.pcs
     #end if
-    #if str($projection):
-    --projection $projection
+    #if str($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
-    $unrelated
-    $build
-    $cluster
-    $rplot
-
+    ## 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,binary" label="Binary Genotype File" />
-        <param name="family" type="data" format="lped,txt" label="Family File" />
-        <param name="map" type="data" format="tabular" label="Map File" />
+        <param name="genotype" type="data" format="pbed" label="Binary Genotype File" help="Generated by PLINK" />
         <!-- Beginning of the optional paramters -->
-        <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" />
-        <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." />
-        <param argument="--degree" type="integer" min="0" optional="true" label="Degrees of relatedness" help="Filters relative pairs based on kinship coefficients." />
-        <param argument="--projection" type="integer" min="0" optional="true" label="Projection N" help="Includes the first N samples of a subset." />
-        <param argument="--unrelated" type="boolean" truevalue="--unrelated" falsevalue="" label="Unrelated Option" help="Extract a list of unrelated individuals." />
-        <param argument="--build" type="boolean" truevalue="--build" falsevalue="" label="Reconstruct Pedigree" help="Reconstructs pedigrees using SNP data" />
-        <param argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" label="Cluster Parameter" help="Clusters relatives into families by generating an updateid file." />
-        <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 name="use_log" type="boolean" checked="false" label="Output a Log?" />
+        <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 ${on_string}: Metrics">
-            <discover_datasets pattern="king(?P&lt;designation&gt;.+)\.txt" format="txt"  />
+            <discover_datasets pattern="king(?P&lt;name&gt;.+)\.txt" format="txt"  />
+            <discover_datasets pattern="king\.(?P&lt;name&gt;.+)" format="txt"  />
+            <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.plink" format="plink" />
+            <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.R" format="txt" />
         </collection>
         <collection name="kingoutput_log" type="list" label="${tool.name} on ${on_string}: Metrics Logs" >
             <filter>use_log == True</filter>
-            <discover_datasets pattern="king(?P&lt;designation&gt;.+)\.log" format="txt" />
+            <discover_datasets pattern="king(?P&lt;name&gt;.+)\.log" format="txt" />
+            <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.Rout" format="txt" />
         </collection>
         <collection name="kingoutput_pdf" type="list" label="${tool.name} on ${on_string}: Plots">
-            <discover_datasets pattern="king_(?P&lt;designation&gt;.+)\.pdf" format="pdf" />
+            <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>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="related" value="true" />
+            <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>
@@ -88,12 +272,18 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="related" value="true" />
-            <param name="degree" value="2" />
+            <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>
@@ -105,13 +295,21 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="related" value="true" />
-            <param name="degree" value="2" />
-            <param name="rplot" value="true" />
+            <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>
@@ -125,11 +323,15 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="duplicate" value="true" />
+            <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>
@@ -139,11 +341,15 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="kinship" value="true" />
+            <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>
@@ -153,12 +359,18 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="related" value="true" />
-            <param name="projection" value="100000" />
+            <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>
@@ -171,11 +383,15 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="ibdseg" value="true" />
+            <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>
@@ -186,13 +402,21 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="ibdseg" value="true" />
-            <param name="degree" value="3" />
-            <param name="rplot" value="true" />
+            <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>
@@ -204,11 +428,15 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="ibs" value="true" />
+            <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>
@@ -222,11 +450,15 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="homog" value="true" />
+            <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>
@@ -237,11 +469,15 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="unrelated" value="true" />
+            <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>
@@ -252,12 +488,18 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="unrelated" value="true" />
-            <param name="degree" value="2" />
+            <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>
@@ -268,11 +510,15 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="build" value="true" />
+            <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>
@@ -283,12 +529,18 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="build" value="true" />
-            <param name="degree" value="2" />
+            <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>
@@ -299,11 +551,15 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="genotype" value="new.6000.bed"/>
-            <param name="family" value="new.6000.fam"/>
-            <param name="map" value="new.6000.bim"/>
-            <param name="cluster" value="true" />
+            <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>
@@ -313,12 +569,126 @@
                 </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.
+    `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>
@@ -326,3 +696,4 @@
         <citation type="doi">10.1093/bioinformatics/btq559</citation>
     </citations>
 </tool>
+