Mercurial > repos > iuc > king

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

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 1c50106137c5b3260f18864ac9084056fa91ec80"
author iuc
date Mon, 18 Apr 2022 18:04:56 +0000
parents ec2bc87ebd7b
children
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
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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
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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
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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
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4 <macros>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
5 <token name="@TOOL_VERSION@">2.2.7</token>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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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
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7 </macros>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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8 <requirements>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
9 <requirement type="package" version="@TOOL_VERSION@">king</requirement>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
10 <requirement type="package" version="1.8.5">r-kinship2</requirement>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
11 <requirement type="package" version="1.3.0">r-igraph</requirement>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
12 <requirement type="package" version="1.7_9">r-e1071</requirement>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
13 </requirements>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
14 <version_command>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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15 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
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diff changeset
16 </version_command>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
17 <command detect_errors="exit_code"><![CDATA[
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
18 ln -s '$genotype' input.bed &&
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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19
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
20 #if $opt_int.family:
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
21 ln -s '$opt_int.family' input.fam &&
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
22 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
23 #if $opt_int.map:
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
24 ln -s '$opt_int.map' input.bim &&
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
25 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
26 #if $gen_rsk.model:
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
27 ln -s '$gen_rsk.model' input.model &&
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
28 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
29 ## General Input
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
30 king -b input.bed
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
31 ## Close Relative Inference
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
32 $close_rel_i.related
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
33 $close_rel_i.duplicate
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
34 ## Pairwise Relatedness Inference
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
35 $pair_rel_i.kinship
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
36 $pair_rel_i.ibdseg
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
37 $pair_rel_i.ibs
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
38 $pair_rel_i.homog
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
39 ## Inference Parameter
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
40 #if str($inf_param.degree):
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
41 --degree $inf_param.degree
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
42 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
43 #if str($inf_param.seglength):
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
44 --seglength $inf_param.seglength
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
45 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
46 ## Relationship Application
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
47 $rel_app.unrelated
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
48 $rel_app.cluster
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
49 $rel_app.build
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
50 ## QC Report
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
51 #if str($qc_rep.callrateN):
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
52 --callrateN $callrateN
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
53 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
54 #if str($qc_rep.callrateM):
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
55 --callrateM $callrateM
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
56 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
57 ## Population Structure
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
58 $pop_str.pca
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
59 $pop_str.mds
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
60 ## Structure Parameter
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
61 #if str($str_par.pcs)
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
62 --pcs $str_par.pcs
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
63 #end if
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
64 #if str($str_par.projection)
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
65 --projection $str_par.projection
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
66 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
67 ## Disease Assosciation
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
68 $dis_ass.tdt
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
69 ## Quantitiative Trait Association
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
70 $qnt_trt.mtscore
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
71 ## Association Model
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
72 #if str($ass_mod.trait)
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
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73 --trait $ass_mod.trait
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
74 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
75 #if str($ass_mod.covariate)
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
76 --covariate $ass_mod.covariate
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
77 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
78 ## Association parameter
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
79 $ass_par.invnorm
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
80 #if str($ass_par.maxP)
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
81 --maxP $ass_par.maxP
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
82 #end if
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
83 ## Genetic Risk Score
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
84 $gen_rsk.risk
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
85 #if $gen_rsk.model:
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
86 --model input.model
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
87 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
88 #if str($gen_rsk.prevalence)
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
89 --prevalence $gen_rsk.prevalence
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
90 #end if
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
91 $gen_rsk.noflip
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
92 ## Computing parameter
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
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93 --cpus "\${GALAXY_SLOTS:-4}"
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94 ## Optional Input
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95 #if $opt_int.family
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96 --fam input.fam
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97 #end if
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98 #if $opt_int.map
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99 --bim input.bim
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100 #end if
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101 #if $opt_int.sexchr
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102 --sexchr $opt_int.sexchr
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103 #end if
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104 ## Output
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105 $opt_par.rplot
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106 $opt_par.pngplot
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107 $opt_par.plink
0
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108 > '$kingoutlog'
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109 ]]></command>
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110 <inputs>
1
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111 <param name="genotype" type="data" format="pbed" label="Binary Genotype File" help="Generated by PLINK" />
0
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112 <!-- Beginning of the optional paramters -->
1
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113 <section name="close_rel_i" title="Close Relative Inference" >
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114 <param argument="--related" type="boolean" truevalue="--related" falsevalue=""
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115 label="Relationship Inference"
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116 help="Implements the fastest and integrated relationship inference." />
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117 <param argument="--duplicate" type="boolean" truevalue="--duplicate" falsevalue=""
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118 label="Duplicate Analysis"
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119 help="Implements the fastest (and accurate) algorithm to identify duplicates or MZ twins" />
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120 </section>
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121 <!-- Despite many of the below parameters being grouped together, they can all
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122 surprisingly be used independently of one another, i.e. no mutual exclusivity that I can see -->
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123 <section name="pair_rel_i" title="Pairwise Relative Inference" >
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124 <param argument="--kinship" type="boolean" truevalue="--kinship" falsevalue=""
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125 label="Kinship Inference"
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126 help="Estimates pair-wise kinship coefficients" />
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127 <param argument="--ibdseg" type="boolean" truevalue="--ibdseg" falsevalue=""
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128 label="IBD Segment Analysis"
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129 help="IBD segment analysis determines all IBD (IBD1 and IBD2) segments shared between relatives" />
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130 <param argument="--ibs" type="boolean" truevalue="--ibs" falsevalue=""
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131 label="IBS Summary Statistics"
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132 help="Counts and average of IBS" />
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133 <param argument="--homog" type="boolean" truevalue="--homog" falsevalue=""
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134 label="Homogeneous Population"
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135 help="Estimates pair-wise kinship coefficients assuming a homogeneous population." />
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136 </section>
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137 <section name="inf_param" title="Inference Parameter" >
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138 <param argument="--degree" type="integer" min="0" optional="true"
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139 label="Degrees of relatedness"
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140 help="Filters relative pairs based on kinship coefficients." />
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141 <param argument="--seglength" type="integer" min="1" optional="true"
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142 label="Minimum IBD segments"
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143 help="specifies the minimum length of IDB segments that are considered towards the relationship inference" />
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144 </section>
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145 <section name="rel_app" title="Relationship Application" >
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146 <param argument="--unrelated" type="boolean" truevalue="--unrelated" falsevalue=""
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147 label="Unrelated Option"
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148 help="Extract a list of unrelated individuals." />
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149 <param argument="--cluster" type="boolean" truevalue="--cluster" falsevalue=""
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150 label="Cluster Parameter"
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151 help="Clusters relatives into families by generating an updateid file." />
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152 <param argument="--build" type="boolean" truevalue="--build" falsevalue=""
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153 label="Reconstruct Pedigree"
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154 help="Reconstructs pedigrees using SNP data" />
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155 </section>
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156 <section name="qc_rep" title="QC Report" >
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157 <param argument="--callrateN" type="integer" min="1" optional="true"
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158 label="Set the N callrate" />
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159 <param argument="--callrateM" type="integer" min="1" optional="true"
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160 label="Set the M callrate" />
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161 </section>
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162 <section name="pop_str" title="Population Structure" >
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163 <param argument="--pca" type="boolean" truevalue="--pca" falsevalue=""
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164 label="Add PCA as dimension reduction algorithm" />
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165 <param argument="--mds" type="boolean" truevalue="--mds" falsevalue=""
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166 label="Add MDS as dimension reduction algorithm" />
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167 </section>
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168 <section name="str_par" title="Structure Parameter" >
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169 <!-- Ye, all options can be selected here, apparently... -->
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170 <param argument="--pcs" type="integer" min="1" optional="true"
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171 label="Number of Principal Components to use"
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172 help="allow the specification of the number of PCs with a default value of 10." />
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173 <param argument="--projection" type="integer" min="0" optional="true"
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174 label="Projection N"
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175 help="Includes the first N samples of a subset." />
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176 </section>
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177 <section name="dis_ass" title="Disease Association" >
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178 <param argument="--tdt" type="boolean" truevalue="--tdt" falsevalue=""
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179 label="Transmission/Disequilibrium Test"
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180 help="implements the well-known Transmission/Disequilibrium Test for family data that consist of parent-affected child trios." />
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181 </section>
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182 <section name="qnt_trt" title="Quantitative Trait Association" >
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183 <param argument="--mtscore" type="boolean" truevalue="--mtscore" falsevalue=""
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184 label="Score Test between SNP and quantitative trait"
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185 help="Only association results with P value less than 5E-8 are printed out, including both cis- and trans- effect associations. "/>
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186 </section>
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187 <section name="ass_mod" title="Association Model" >
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188 <param argument="--trait" type="text" optional="true"
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189 label="Trait names"
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190 help="Specifies the trait names to be analyzed in the association analysis." />
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191 <param argument="--covariate" type="text" optional="true"
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192 label="Covariate names"
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193 help="Specifies the covariate names to be adjusted in the association analysis" />
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194 </section>
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195 <section name="ass_par" title="Association Parameter" >
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196 <param argument="--invnorm" type="boolean" truevalue="--invnorm" falsevalue=""
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197 label="Normal Transformation"
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198 help="Carries out inverse normal transformation for quantitative traits prior to association analysis."/>
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199 <param argument="--maxP" type="float" min="0" optional="true"
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200 label="maximum P values"
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201 help="specifies the maximum P values to print out in the output files."/>
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202 </section>
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203 <section name="gen_rsk" title="Genetic Risk Score" >
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204 <param argument="--risk" type="boolean" truevalue="--risk" falsevalue=""
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205 label="Predict Disease Risk"
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206 help="predicts disease risks for each individual according to the GRS risk model" />
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207 <param name="model" type="data" format="txt,tabular" label="GRS Risk Model file" optional="true" />
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208 <param argument="--prevalence" type="float" min="0" optional="true"
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209 label="Disease prevalence" />
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210 <param argument="--noflip" type="boolean" truevalue="--noflip" falsevalue=""
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211 label="No Flip"
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212 help="If strands of genotype data are already consistent with model, enable this." />
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213 </section>
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214 <section name="opt_int" title="Optional Input" >
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215 <param name="family" type="data" format="lped,txt" label="Family File" optional="true" />
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216 <param name="map" type="data" format="tabular" label="Map File" optional="true" />
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217 <param argument="--sexchr" type="integer" min="0" optional="true"
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218 label="Pair number of the Sex Chromosome."
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219 help="specifies the pair number of the sex chromosome, which should be userful for non-human species. The default sex chromosome is 23." />
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220 </section>
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221 <section name="opt_par" title="Optional Parameter" >
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222 <param argument="--rplot" type="boolean" truevalue="--rplot" falsevalue=""
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223 label="R Code and Plots"
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224 help="Generates R code first and then calls R program to make plots in a PDF file." />
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225 <param argument="--pngplot" type="boolean" truevalue="--pngplot" falsevalue=""
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226 label="R Code and Plots in PNG format"
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227 help="Generates R code first and then calls R program to make plots in a PNG file for certain applications." />
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228 <param argument="--plink" type="boolean" truevalue="--plink" falsevalue=""
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229 label="Output data in PLINK format" />
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230 </section>
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231 <param name="use_log" type="boolean" checked="false"
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232 label="Output a Log?" />
0
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233 </inputs>
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234 <outputs>
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235 <data name="kingoutlog" format="txt" label="${tool.name} on ${on_string} : Log" >
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236 <filter>use_log == True</filter>
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237 </data>
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238 <collection name="kingoutput_txt" type="list" label="${tool.name} on ${on_string}: Metrics">
1
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239 <discover_datasets pattern="king(?P&lt;name&gt;.+)\.txt" format="txt" />
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240 <discover_datasets pattern="king\.(?P&lt;name&gt;.+)" format="txt" />
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241 <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.plink" format="plink" />
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242 <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.R" format="txt" />
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
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243 </collection>
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244 <collection name="kingoutput_log" type="list" label="${tool.name} on ${on_string}: Metrics Logs" >
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245 <filter>use_log == True</filter>
1
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246 <discover_datasets pattern="king(?P&lt;name&gt;.+)\.log" format="txt" />
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247 <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.Rout" format="txt" />
0
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248 </collection>
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249 <collection name="kingoutput_pdf" type="list" label="${tool.name} on ${on_string}: Plots">
1
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250 <filter>opt_par["rplot"] or opt_par["pngplot"]</filter>
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251 <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.pdf" format="pdf" />
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252 <discover_datasets pattern="king_(?P&lt;name&gt;.+)\.png" format="png" />
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
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253 </collection>
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254 </outputs>
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255 <tests>
1
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256 <test expect_num_outputs="3">
0
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257 <param name="genotype" value="new.6000.bed"/>
1
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258 <section name="opt_int" >
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259 <param name="family" value="new.6000.fam"/>
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260 <param name="map" value="new.6000.bim"/>
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261 </section>
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262 <section name="close_rel_i" >
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263 <param name="related" value="true" />
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264 </section>
0
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265 <param name="use_log" value="true" />
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266 <output name="kingoutlog">
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267 <assert_contents>
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268 <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is"/>
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269 <has_text text="Information of these chromosomal segments can be found in file kingallsegs.txt" />
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270 <has_text text="--related" />
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271 <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" />
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272 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
273 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
274 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
275 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
276 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
277 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
278 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
279 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
280 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
281 <section name="close_rel_i" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
282 <param name="related" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
283 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
284 <section name="inf_param" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
285 <param name="degree" value="2" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
286 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
287 <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
288 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
289 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
290 <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
291 <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
292 <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
293 <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
294 <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
295 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
296 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
297 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
298 <test expect_num_outputs="4">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
299 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
300 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
301 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
302 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
303 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
304 <section name="close_rel_i" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
305 <param name="related" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
306 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
307 <section name="inf_param" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
308 <param name="degree" value="2" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
309 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
310 <section name="opt_par" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
311 <param name="rplot" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
312 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
313 <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
314 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
315 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
316 <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
317 <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
318 <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
319 <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
320 <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
321 <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
322 <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
323 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
324 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
325 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
326 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
327 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
328 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
329 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
330 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
331 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
332 <section name="close_rel_i" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
333 <param name="duplicate" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
334 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
335 <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
336 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
337 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
338 <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
339 <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
340 <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
341 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
342 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
343 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
344 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
345 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
346 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
347 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
348 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
349 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
350 <section name="pair_rel_i" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
351 <param name="kinship" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
352 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
353 <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
354 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
355 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
356 <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
357 <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
358 <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
359 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
360 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
361 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
362 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
363 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
364 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
365 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
366 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
367 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
368 <section name="close_rel_i" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
369 <param name="related" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
370 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
371 <section name="str_par" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
372 <param name="projection" value="100000" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
373 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
374 <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
375 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
376 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
377 <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
378 <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
379 <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
380 <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
381 <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
382 <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
383 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
384 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
385 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
386 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
387 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
388 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
389 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
390 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
391 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
392 <section name="pair_rel_i" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
393 <param name="ibdseg" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
394 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
395 <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
396 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
397 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
398 <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
399 <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
400 <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
401 <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
402 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
403 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
404 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
405 <test expect_num_outputs="4">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
406 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
407 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
408 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
409 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
410 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
411 <section name="pair_rel_i" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
412 <param name="ibdseg" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
413 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
414 <section name="inf_param" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
415 <param name="degree" value="3" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
416 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
417 <section name="opt_par" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
418 <param name="rplot" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
419 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
420 <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
421 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
422 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
423 <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
424 <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
425 <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
426 <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
427 <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
428 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
429 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
430 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
431 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
432 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
433 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
434 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
435 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
436 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
437 <section name="pair_rel_i" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
438 <param name="ibs" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
439 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
440 <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
441 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
442 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
443 <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
444 <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
445 <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
446 <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
447 <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
448 <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
449 <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
450 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
451 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
452 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
453 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
454 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
455 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
456 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
457 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
458 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
459 <section name="pair_rel_i" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
460 <param name="homog" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
461 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
462 <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
463 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
464 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
465 <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
466 <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
467 <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
468 <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
469 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
470 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
471 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
472 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
473 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
474 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
475 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
476 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
477 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
478 <section name="rel_app" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
479 <param name="unrelated" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
480 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
481 <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
482 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
483 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
484 <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
485 <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
486 <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
487 <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
488 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
489 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
490 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
491 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
492 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
493 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
494 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
495 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
496 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
497 <section name="rel_app" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
498 <param name="unrelated" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
499 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
500 <section name="inf_param" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
501 <param name="degree" value="2" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
502 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
503 <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
504 <output name="kingoutlog" >
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
505 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
506 <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
507 <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
508 <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
509 <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
510 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
511 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
512 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
513 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
514 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
515 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
516 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
517 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
518 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
519 <section name="rel_app" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
520 <param name="build" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
521 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
522 <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
523 <output name="kingoutlog" >
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
524 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
525 <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
526 <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
527 <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
528 <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
529 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
530 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
531 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
532 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
533 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
534 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
535 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
536 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
537 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
538 <section name="rel_app" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
539 <param name="build" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
540 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
541 <section name="inf_param" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
542 <param name="degree" value="2" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
543 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
544 <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
545 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
546 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
547 <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
548 <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
549 <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
550 <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
551 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
552 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
553 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
554 <test expect_num_outputs="3">
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
555 <param name="genotype" value="new.6000.bed"/>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
556 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
557 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
558 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
559 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
560 <section name="rel_app" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
561 <param name="cluster" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
562 </section>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
563 <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
564 <output name="kingoutlog">
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
565 <assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
566 <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
567 <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
568 <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
569 </assert_contents>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
570 </output>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
571 </test>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
572 <test> <!-- risk prediction -->
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
573 <param name="genotype" value="new.6000.bed"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
574 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
575 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
576 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
577 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
578 <section name="gen_rsk">
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
579 <param name="model" ftype="txt" value="test.model" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
580 <param name="risk" value="true"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
581 <param name="prevalence" value="0.004"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
582 <param name="noflip" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
583 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
584 <param name="use_log" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
585 <output name="kingoutlog" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
586 <assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
587 <has_text text="rs2602970 11 T A 0.265 0.403 C T 0.474 SWITCHED" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
588 <has_text text="rs1161312 17 C T 0.459 0.295 G A 0.408 FLIPPED" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
589 </assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
590 </output>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
591 <output_collection name="kingoutput_txt" count="1">
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
592 <element name="grs" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
593 <assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
594 <has_text text="13292 NA07014 1.000 1.000 4.917 3.243 0.0006 0.9927" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
595 </assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
596 </element>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
597 </output_collection>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
598 </test>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
599 <test expect_num_outputs="3" > <!-- association mapping 1 -->
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
600 <param name="genotype" value="new.6000.bed"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
601 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
602 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
603 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
604 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
605 <section name="dis_ass">
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
606 <param name="tdt" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
607 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
608 <param name="use_log" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
609 <output name="kingoutlog" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
610 <assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
611 <has_text text="There are no parent-affected-offspring trios in the data." />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
612 </assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
613 </output>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
614 </test>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
615 <test expect_num_outputs="3"> <!-- association mapping 2 -->
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
616 <param name="genotype" value="new.6000.bed"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
617 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
618 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
619 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
620 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
621 <section name="ass_mod">
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
622 <param name="covariate" value="," />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
623 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
624 <section name="qnt_trt" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
625 <param name="mtscore" value="false"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
626 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
627 <section name="ass_par">
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
628 <param name="invnorm" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
629 <param name="maxP" value="5e-8"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
630 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
631 <param name="use_log" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
632 <output name="kingoutlog" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
633 <assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
634 <has_text_matching expression="Inference\s+0\s+1\s+1\s+0" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
635 </assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
636 </output>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
637 <output_collection name="kingoutput_txt" count="3" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
638 <element name="allsegs" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
639 <assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
640 <has_text_matching expression="1\s+1\s+51\.\d+\s+95\.\d+\s+44\.\d+\s+294\s+rs7534689\s+rs1858111" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
641 </assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
642 </element>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
643 <element name="kin0" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
644 <assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
645 <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" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
646 </assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
647 </element>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
648 </output_collection>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
649 </test>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
650 <test expect_num_outputs="4" > <!-- ancestry inferrence -->
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
651 <param name="genotype" value="new.6000.bed"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
652 <section name="opt_int" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
653 <param name="family" value="new.6000.fam"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
654 <param name="map" value="new.6000.bim"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
655 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
656 <section name="pop_str">
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
657 <param name="pca" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
658 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
659 <section name="str_par" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
660 <param name="projection" value="1"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
661 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
662 <section name="opt_par">
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
663 <param name="rplot" value="true"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
664 <param name="pngplot" value="true"/>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
665 </section>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
666 <param name="use_log" value="true" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
667 <output name="kingoutlog">
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
668 <assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
669 <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+" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
670 </assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
671 </output>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
672 <output_collection name="kingoutput_txt" count="3" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
673 <element name="pc">
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
674 <assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
675 <has_text_matching expression="Y117\s+NA19239\s+0\s+0\s+1\s+1\s+.*" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
676 </assert_contents>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
677 </element>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
678 </output_collection>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
679 <output_collection name="kingoutput_log" count="2" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
680 <output_collection name="kingoutput_pdf" count="1" >
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
681 <element name="pcplot" value="king_pcplot.png" compare="sim_size" delta="2500" />
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
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diff changeset
682 </output_collection>
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
683 </test>
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
684 </tests>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
685 <help><![CDATA[
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
parents:
diff changeset
686
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
687 `KING <http://people.virginia.edu/~wc9c/KING/>`_ is a toolset that makes use of
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
688 high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
parents: 0
diff changeset
689 sequencing project. Applications of KING include family relationship inference and
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
690 pedigree error checking, quality control, population substructure identification,
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
iuc
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diff changeset
691 forensics, gene mapping, etc.
0
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
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692
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
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diff changeset
693 ]]>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
694 </help>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
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diff changeset
695 <citations>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
696 <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"
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diff changeset
697 </citations>
ec2bc87ebd7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
iuc
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diff changeset
698 </tool>
1
1932808c6fab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80"
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diff changeset
699