Mercurial > repos > iuc > king

annotate king.xml @ 0:ec2bc87ebd7b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
author iuc
date Tue, 16 Nov 2021 20:14:31 +0000
parents
children 1932808c6fab
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
1 <?xml version="1.0" encoding="utf-8"?>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
2 <tool id="king" name="KING" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
3 <description>Kinship-based INference for GWAS</description>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
4 <macros>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
5 <token name="@TOOL_VERSION@">2.2.4</token>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
6 <token name="@VERSION_SUFFIX@">0</token>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
7 </macros>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
8 <requirements>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
9 <requirement type="package" version="@TOOL_VERSION@">king</requirement>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
10 <requirement type="package" version="1.6.4">r-kinship2</requirement>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
11 <requirement type="package" version="1.2.2">r-igraph</requirement>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
12 </requirements>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
13 <version_command>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
14 king | head -1 | cut -d' ' -f 2
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
15 </version_command>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
16 <command detect_errors="exit_code"><![CDATA[
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
17 ln -s '$genotype' input.bed &&
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
18 ln -s '$family' input.fam &&
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
19 ln -s '$map' input.bim &&
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
20
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
21 king -b input.bed --fam input.fam --bim input.bim
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
22 $related
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
23 $duplicate
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
24 $kinship
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
25 $ibdseg
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
26 $ibs
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
27 $homog
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
28 #if str($degree):
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
29 --degree $degree
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
30 #end if
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
31 #if str($projection):
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
32 --projection $projection
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
33 #end if
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
34 $unrelated
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
35 $build
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
36 $cluster
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
37 $rplot
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
38
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
39 > '$kingoutlog'
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
40 ]]></command>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
41 <inputs>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
42 <param name="genotype" type="data" format="pbed,binary" label="Binary Genotype File" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
43 <param name="family" type="data" format="lped,txt" label="Family File" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
44 <param name="map" type="data" format="tabular" label="Map File" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
45 <!-- Beginning of the optional paramters -->
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
46 <param argument="--related" type="boolean" truevalue="--related" falsevalue="" label="Relationship Inference" help="Implements the fastest and integrated relationship inference." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
47 <param argument="--duplicate" type="boolean" truevalue="--duplicate" falsevalue="" label="Duplicate Analysis" help="Implements the fastest (and accurate) algorithm to identify duplicates or MZ twins" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
48 <param argument="--kinship" type="boolean" truevalue="--kinship" falsevalue="" label="Kinship Inference" help="Estimates pair-wise kinship coefficients" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
49 <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" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
50 <param argument="--ibs" type="boolean" truevalue="--ibs" falsevalue="" label="IBS Summary Statistics" help="Counts and average of IBS" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
51 <param argument="--homog" type="boolean" truevalue="--homog" falsevalue="" label="Homogeneous Population" help="Estimates pair-wise kinship coefficients assuming a homogeneous population." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
52 <param argument="--degree" type="integer" min="0" optional="true" label="Degrees of relatedness" help="Filters relative pairs based on kinship coefficients." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
53 <param argument="--projection" type="integer" min="0" optional="true" label="Projection N" help="Includes the first N samples of a subset." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
54 <param argument="--unrelated" type="boolean" truevalue="--unrelated" falsevalue="" label="Unrelated Option" help="Extract a list of unrelated individuals." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
55 <param argument="--build" type="boolean" truevalue="--build" falsevalue="" label="Reconstruct Pedigree" help="Reconstructs pedigrees using SNP data" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
56 <param argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" label="Cluster Parameter" help="Clusters relatives into families by generating an updateid file." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
57 <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." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
58 <param name="use_log" type="boolean" checked="false" label="Output a Log?" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
59 </inputs>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
60 <outputs>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
61 <data name="kingoutlog" format="txt" label="${tool.name} on ${on_string} : Log" >
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
62 <filter>use_log == True</filter>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
63 </data>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
64 <collection name="kingoutput_txt" type="list" label="${tool.name} on ${on_string}: Metrics">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
65 <discover_datasets pattern="king(?P&lt;designation&gt;.+)\.txt" format="txt" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
66 </collection>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
67 <collection name="kingoutput_log" type="list" label="${tool.name} on ${on_string}: Metrics Logs" >
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
68 <filter>use_log == True</filter>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
69 <discover_datasets pattern="king(?P&lt;designation&gt;.+)\.log" format="txt" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
70 </collection>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
71 <collection name="kingoutput_pdf" type="list" label="${tool.name} on ${on_string}: Plots">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
72 <discover_datasets pattern="king_(?P&lt;designation&gt;.+)\.pdf" format="pdf" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
73 </collection>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
74 </outputs>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
75 <tests>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
76 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
77 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
78 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
79 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
80 <param name="related" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
81 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
82 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
83 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
84 <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
85 <has_text text="Information of these chromosomal segments can be found in file kingallsegs.txt" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
86 <has_text text="--related" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
87 <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
88 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
89 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
90 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
91 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
92 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
93 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
94 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
95 <param name="related" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
96 <param name="degree" value="2" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
97 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
98 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
99 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
100 <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
101 <has_text text="Information of these chromosomal segments can be found in file kingallsegs.txt" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
102 <has_text text="--related" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
103 <has_text text="--degree 2" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
104 <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
105 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
106 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
107 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
108 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
109 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
110 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
111 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
112 <param name="related" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
113 <param name="degree" value="2" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
114 <param name="rplot" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
115 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
116 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
117 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
118 <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
119 <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
120 <has_text text="--related" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
121 <has_text text="--degree 2" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
122 <has_text text="--rplot" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
123 <has_text text="(with 6000 SNPs): 8 pairs of relatives are detected (with kinship > 0.0625)" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
124 <has_text text="Relationship summary (total relatives: 0 by pedigree, 6 by inference)" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
125 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
126 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
127 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
128 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
129 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
130 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
131 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
132 <param name="duplicate" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
133 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
134 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
135 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
136 <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
137 <has_text text="--duplicate" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
138 <has_text text="No duplicates are found with heterozygote concordance rate > 80%." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
139 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
140 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
141 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
142 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
143 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
144 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
145 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
146 <param name="kinship" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
147 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
148 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
149 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
150 <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
151 <has_text text="--kinship" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
152 <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
153 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
154 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
155 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
156 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
157 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
158 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
159 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
160 <param name="related" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
161 <param name="projection" value="100000" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
162 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
163 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
164 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
165 <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
166 <has_text text="--related" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
167 <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
168 <has_text text="PLINK pedigrees loaded: 332 samples" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
169 <has_text text="PLINK maps loaded: 6000 SNPs" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
170 <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
171 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
172 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
173 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
174 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
175 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
176 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
177 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
178 <param name="ibdseg" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
179 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
180 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
181 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
182 <has_text text="--ibdseg" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
183 <has_text text="Sample pairs without any long IBD segments (>10Mb) are excluded." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
184 <has_text text="IBD segments saved in a gzipped file king.segments.gz" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
185 <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
186 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
187 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
188 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
189 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
190 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
191 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
192 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
193 <param name="ibdseg" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
194 <param name="degree" value="3" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
195 <param name="rplot" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
196 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
197 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
198 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
199 <has_text text="--ibdseg" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
200 <has_text text="--rplot" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
201 <has_text text="--degree 3" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
202 <has_text text="Summary statistics of IBD segments for individual pairs saved in file king.seg" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
203 <has_text text="Genotype data consist of 6000 autosome SNPs" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
204 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
205 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
206 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
207 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
208 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
209 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
210 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
211 <param name="ibs" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
212 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
213 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
214 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
215 <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
216 <has_text text="Within-family IBS data saved in file king.ibs" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
217 <has_text text="--ibs" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
218 <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
219 <has_text text="Information of these chromosomal segments can be found in file kingallsegs.txt" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
220 <has_text text="Between-family IBS data saved in file king.ibs0" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
221 <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
222 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
223 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
224 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
225 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
226 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
227 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
228 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
229 <param name="homog" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
230 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
231 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
232 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
233 <has_text text="Autosome genotypes stored in 375 words for each of 332 individuals." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
234 <has_text text="--homo" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
235 <has_text text="Within-family kinship data saved in file king.kin" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
236 <has_text text="Genotype data consist of 6000 autosome SNPs" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
237 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
238 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
239 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
240 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
241 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
242 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
243 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
244 <param name="unrelated" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
245 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
246 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
247 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
248 <has_text text="--unrelated" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
249 <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
250 <has_text text="Y028,Y117" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
251 <has_text text="An alternative list of 114 to-be-removed individuals saved in file kingunrelated_toberemoved.txt" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
252 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
253 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
254 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
255 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
256 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
257 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
258 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
259 <param name="unrelated" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
260 <param name="degree" value="2" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
261 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
262 <output name="kingoutlog" >
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
263 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
264 <has_text text="--unrelated" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
265 <has_text text="--degree 2" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
266 <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
267 <has_text text="An alternative list of 114 to-be-removed individuals saved in file kingunrelated_toberemoved.txt" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
268 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
269 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
270 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
271 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
272 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
273 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
274 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
275 <param name="build" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
276 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
277 <output name="kingoutlog" >
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
278 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
279 <has_text text="--build" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
280 <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
281 <has_text text="Update-ID information is saved in file kingupdateids.txt" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
282 <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
283 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
284 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
285 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
286 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
287 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
288 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
289 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
290 <param name="build" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
291 <param name="degree" value="2" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
292 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
293 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
294 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
295 <has_text text="--build" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
296 <has_text text="--degree 2" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
297 <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
298 <has_text text="Update-parent information is saved in file kingupdateparents.txt" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
299 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
300 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
301 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
302 <test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
303 <param name="genotype" value="new.6000.bed"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
304 <param name="family" value="new.6000.fam"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
305 <param name="map" value="new.6000.bim"/>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
306 <param name="cluster" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
307 <param name="use_log" value="true" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
308 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
309 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
310 <has_text text="--cluster" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
311 <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
312 <has_text text="Pair-wise relatedness in newly clustered families saved in kingcluster.kin." />
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
313 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
314 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
315 </test>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
316 </tests>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
317 <help><![CDATA[
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
318
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
319 `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)
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
320 or a sequencing project. Applications of KING include family relationship inference and pedigree error checking,
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
321 quality control, population substructure identification, forensics, gene mapping, etc.
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
322
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
323 ]]>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
324 </help>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
325 <citations>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
326 <citation type="doi">10.1093/bioinformatics/btq559</citation>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
327 </citations>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
328 </tool>