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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 418c096b5dcaca9d35e762f5ad185ffd28af4490
author iuc
date Fri, 04 Oct 2024 08:48:06 +0000
parents eae84c835026
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
64a2c5a3acf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 418c096b5dcaca9d35e762f5ad185ffd28af4490
iuc
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1 <tool id="merlin" name="Tool for Linkage Analysis" version="@TOOL_VERSION@.3">
1
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
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2 <macros>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
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3 <token name="@TOOL_VERSION@">1.1.2</token>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
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4 </macros>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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5 <xrefs>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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6 <xref type="bio.tools">merlin</xref>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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7 </xrefs>
0
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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8 <requirements>
1
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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9 <requirement type="package" version="@TOOL_VERSION@">merlin</requirement>
0
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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10 </requirements>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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11 <command detect_errors="exit_code"><![CDATA[
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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12 merlin -p '$pname' -m '$mname' -d '$dname' --quiet --error --best --npl '$markerNames'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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13
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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14 #if $minStep
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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15 --minStep '$minStep'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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16 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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17
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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18 #if $maxStep
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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19 --maxStep '$maxStep'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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20 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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21
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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22 #if $steps
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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23 --steps '$steps'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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24 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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25
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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26 #if $grid
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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27 --grid '$grid'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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28 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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29
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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30 #if $start
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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31 --start '$start'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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32 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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33
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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34 #if $stop
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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35 --stop '$stop'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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36 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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37
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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38 #if $randomseed
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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39 -r '$randomseed'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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40 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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41
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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42 #if $allelefrequency.allelefreq.value == "maxlike":
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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43 -fm
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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44 #elif $allelefrequency.allelefreq.value == "founders":
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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45 -ff
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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46 #elif $allelefrequency.allelefreq.value == "individuals":
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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47 -fa
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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48 #elif $allelefrequency.allelefreq.value == "equal":
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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49 -fe
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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50 #elif $allelefrequency.allelefreq.value == "file":
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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51 -f '$allelefrequency.file'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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52 #end if
1
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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53
0
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54 > '$merlinoutput'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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55 ]]></command>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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56 <inputs>
1
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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57 <!-- Select input data file -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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58 <param name="pname" type="data" format="txt" label="Entering Data File" help="Selects input data file, in linkage or QTDT format" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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59 <!-- Select input map file -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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60 <param name="mname" type="data" format="txt" label="Entering Map File" help="File indicating chromosome and centimorgan position for each marker. Use with QTDT format input files." />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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61 <!-- Select input pedigree file -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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62 <param name="dname" type="data" format="txt" label="Entering Pedigree File" help="Selects pedigree file, with genotype, phenotype and family structure information" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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63 <!-- Beginning of the optional parameters -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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64 <param name="markerNames" type="boolean" truevalue="--markerNames" falsevalue="" optional="true" label="For Marker Serial Optional Parameter" help="Useful to eliminate numbers in positions and introduce serial of MRK Number instead." />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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65 <param name="minStep" type="float" optional="true" label="For Minimum Step Optional Parameter" help="Useful to find the minimum value" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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66 <param name="maxStep" type="float" optional="true" label="For Maximum Step Optional Paramter" help="Useful to find the maximum value" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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67 <param name="steps" type="integer" min="0" optional="true" label="n equally spaced locations" help="Carry out analyses at n equally spaced locations to analyse between consecutive markers" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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68 <param name="grid" type="integer" min="0" optional="true" label="n-cM grid of equally spaced locations" help="Carry out analysis along an n-cM grid of equally spaced locations" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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69 <param name="start" type="integer" min="0" optional="true" label="Start analyses" help="Start analyses at pos centiMorgans." />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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70 <param name="stop" type="integer" min="0" optional="true" label="Stop analyses" help="Stop analyses at pos centiMorgans." />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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71 <param name="randomseed" type="integer" min="0" optional="true" label="Random Sequence" help="Selects a different random sequence for simulation and sampling of haplotypes." />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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72 <!-- Beginning of the conditional parameters -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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73 <conditional name="allelefrequency">
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74 <param name="allelefreq" type="select" label="Source for allele frequency information" help="Allele frequencies can be set in one of the four options.">
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75 <option value="maxlike"> Maximum Likelihood </option>
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76 <option value="founders"> Founders </option>
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77 <option value="individuals">All Individuals</option>
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78 <option value="equal">Assume Equal</option>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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79 <option value="file">User File</option>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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80 </param>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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81 <when value="maxlike">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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82 <!-- Nothing to be added. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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83 </when>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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84 <when value="founders">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
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diff changeset
85 <!-- Nothing to be added. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
86 </when>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
87 <when value="individuals">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
88 <!-- Nothing to be added. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
89 </when>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
90 <when value="equal">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
91 <!-- Nothing to be added. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
92 </when>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
93 <when value="file">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
94 <param name="file" type="data" format="tabular" label="User Specified file for Allele frequencies" help="Source for allele frequency information."/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
95 </when>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
96 </conditional>
0
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
97 </inputs>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
98 <outputs>
1
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
99 <!-- Set of outputs along with the formats. -->
3
64a2c5a3acf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 418c096b5dcaca9d35e762f5ad185ffd28af4490
iuc
parents: 2
diff changeset
100 <data name="errors" format="txt" from_work_dir="merlin.err" label="${tool.name} on ${on_string}: merlin.err"/>
64a2c5a3acf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 418c096b5dcaca9d35e762f5ad185ffd28af4490
iuc
parents: 2
diff changeset
101 <data name="flow" format="txt" from_work_dir="merlin.flow" label="${tool.name} on ${on_string}: merlin.flow" />
64a2c5a3acf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 418c096b5dcaca9d35e762f5ad185ffd28af4490
iuc
parents: 2
diff changeset
102 <data name="chromosome" format="txt" from_work_dir="merlin.chr" label="${tool.name} on ${on_string}: merlin.chr" />
1
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
103 <data name="merlinoutput" format="txt" />
0
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
104 </outputs>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
105 <tests>
1
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
106 <test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
107 <!-- No optional parameters used in this test but testing a conditional parameter and random value. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
108 <param name="pname" value="parametric.ped"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
109 <param name="mname" value="parametric.map"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
110 <param name="dname" value="parametric.dat"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
111 <param name="allelefreq" value="file"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
112 <param name="file" value="alle.txt" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
113 <param name="randomseed" value="2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
114 <output name="merlinoutput">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
115 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
116 <has_text text="MRK1 MRK2 MRK3 MRK4 MRK5 MRK6 MRK7 MRK8 MRK9 MRK10" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
117 <not_has_text text="--minStep [2]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
118 <has_line line="Phenotype: VERY_RARE_DISEASE [ALL] (1 family)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
119 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
120 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
121 <output name="chromosome">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
122 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
123 <has_text text="FAMILY 1 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
124 <has_text text="208 (F) 207 (102,101) 305 (208,207) 202 (102,101)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
125 <has_text text="4 : 1 4 : 1 3 : 3 3 : 3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
126 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
127 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
128 <output name="flow">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
129 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
130 <has_text text="FAMILY 1 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
131 <has_text text="101 (F) 102 (F) 201 (F) 203 (F)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
132 <has_text text="A : B C : D E : F G : H" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
133 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
134 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
135 <output name="errors">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
136 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
137 <has_text text="FAMILY PERSON MARKER RATIO" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
138 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
139 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
140 </test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
141 <test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
142 <!-- This test uses markerNames optional parameter and maxlike option in this test case leads to error. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
143 <param name="pname" value="x.ped"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
144 <param name="mname" value="x.map"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
145 <param name="dname" value="x.dat"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
146 <param name="markerNames" value="true" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
147 <!-- Selecting allele frequency can be estimated by counting in founders. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
148 <param name="allelefreq" value="founders"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
149 <param name="randomseed" value="6" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
150 <output name="merlinoutput">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
151 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
152 <has_text text= "MRK1 MRK2 MRK3 MRK4 MRK5 MRK6 MRK7 MRK8 MRK9 MRK10" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
153 <has_text text= "Family: 1 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
154 <has_text text="Family: 2 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
155 <has_text text= "Family: 3 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
156 <has_text text= "Family: 4 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
157 <has_text text= "Family: 5 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
158 <not_has_text text="--minStep [2]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
159 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
160 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
161 <output name="chromosome">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
162 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
163 <has_text text="FAMILY 5 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
164 <has_text text="1 (F) 2 (F) 4 (2,1) 3 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
165 <has_text text="2 : 2 4 : 2 4 : 2 2 : 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
166 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
167 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
168 <output name="flow">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
169 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
170 <has_text text="FAMILY 5 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
171 <has_text text="1 (F) 2 (F) 4 (2,1) 3 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
172 <has_text text="A : B C : D C : A D : A" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
173 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
174 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
175 <output name="errors">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
176 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
177 <has_text text="FAMILY PERSON MARKER RATIO" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
178 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
179 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
180 </test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
181 <test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
182 <!-- This test uses minStep optional parameter -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
183 <param name="pname" value="haplo.ped"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
184 <param name="mname" value="haplo.map"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
185 <param name="dname" value="haplo.dat"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
186 <!-- Selecting allele frequency can be estimated by counting in all individuals. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
187 <param name="allelefreq" value="individuals"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
188 <param name="minStep" value="2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
189 <param name="randomseed" value="5" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
190 <output name="merlinoutput">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
191 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
192 <has_text text= "SNP-1 SNP-2 SNP-3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
193 <has_text text= "--minStep [2.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
194 <not_has_text text="--markerNames [ON]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
195 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
196 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
197 <output name="chromosome">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
198 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
199 <has_text text="FAMILY 3 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
200 <has_text text="1 (F) 2 (F) 3 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
201 <has_text text="1,2A : A2,1 2,1A : A1,2 2,1A | A1,2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
202 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
203 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
204 <output name="flow">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
205 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
206 <has_text text="FAMILY 3 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
207 <has_text text="1 (F) 2 (F) 3 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
208 <has_text text="A : B C : D C : A" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
209 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
210 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
211 <output name="errors">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
212 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
213 <has_text text="FAMILY PERSON MARKER RATIO" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
214 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
215 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
216 </test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
217 <test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
218 <!--This test uses steps optinal parameter -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
219 <param name="pname" value="asp.ped"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
220 <param name="mname" value="asp.map"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
221 <param name="dname" value="asp.dat"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
222 <!-- Selecting allele frequency can be estimated by assuming equal allele frequencies. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
223 <param name="allelefreq" value="equal"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
224 <param name="steps" value="3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
225 <output name="merlinoutput">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
226 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
227 <has_text text= "Phenotype: affection [ALL] (200 families)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
228 <has_text text= "--steps [3]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
229 <not_has_text text="--markerNames [ON]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
230 <not_has_text text="--minStep [2.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
231 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
232 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
233 <output name="chromosome">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
234 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
235 <has_text text= "FAMILY 200 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
236 <has_text text= "1 (F) 2 (F) 4 (2,1) 3 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
237 <has_text text= "4 : 1 4 : 1 4 : 4 1 : 1" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
238 <has_text text=" 3,4A : 3 4,3A : 3 4,3A | A3,4 3 | 3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
239 <has_text text="2,4A : B4,1 4,2A : B1,4 4,2A | A2,4 1,4B | B4,1" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
240 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
241 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
242 <output name="flow">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
243 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
244 <has_text text= "FAMILY 200 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
245 <has_text text= "1 (F) 2 (F) 4 (2,1) 3 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
246 <has_text text= "A : B C : D C : A C : A" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
247 <has_text text="A : B C : D C | A C | A" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
248 <has_text text="A : B C : D C | A C | A" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
249 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
250 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
251 <output name="errors">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
252 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
253 <has_text text="FAMILY PERSON MARKER RATIO" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
254 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
255 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
256 </test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
257 <test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
258 <!-- This test uses grid optional parameter -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
259 <param name="pname" value="sibs.ped"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
260 <param name="mname" value="sibs.map"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
261 <param name="dname" value="sibs.dat"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
262 <param name="allelefreq" value="maxlike"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
263 <param name="grid" value="3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
264 <output name="merlinoutput">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
265 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
266 <has_text text= "SNP_1 SNP_2 SNP_3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
267 <has_text text= "Family: 29 - Founders: 2 - Descendants: 4 - Bits: 6" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
268 <has_text text= "--grid [3.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
269 <not_has_text text="--markerNames [ON]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
270 <not_has_text text="--minStep [2.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
271 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
272 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
273 <output name="chromosome">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
274 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
275 <has_text text="FAMILY 50 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
276 <has_text text="1 (F) 2 (F) 6 (2,1) 5 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
277 <has_text text="2 : 2 1 : 2 1 : 2 2 : 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
278 <has_text text="2 : 1 1 : 1 1 | 2 1 | 1" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
279 <has_text text="2 : 1 1 : 1 1 | 2 1 | 1" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
280 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
281 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
282 <output name="flow">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
283 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
284 <has_text text="FAMILY 50 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
285 <has_text text="1 (F) 2 (F) 6 (2,1) 5 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
286 <has_text text="A : B C : D C : A C : B" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
287 <has_text text="A : B C : D C | A C | B" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
288 <has_text text="A : B C : D C | A C | B" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
289 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
290 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
291 <output name="errors">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
292 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
293 <has_text text="29 4 SNP_1" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
294 <has_text text="29 4 SNP_3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
295 <has_text text="29 5 SNP_3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
296 <has_text text="29 6 SNP_3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
297 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
298 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
299 </test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
300 <test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
301 <!-- This test uses start optional parameter along with a conditional parameter -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
302 <param name="pname" value="assoc.ped"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
303 <param name="mname" value="assoc.map"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
304 <param name="dname" value="assoc.dat"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
305 <param name="allelefreq" value="founders"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
306 <param name="start" value="2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
307 <output name="merlinoutput">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
308 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
309 <has_text text= "--start [2.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
310 <not_has_text text="--markerNames [ON]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
311 <not_has_text text="--minStep [2.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
312 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
313 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
314 <output name="chromosome">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
315 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
316 <has_text text="6 (2,1) 5 (2,1) 4 (2,1) 3 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
317 <has_text text="3 : 3 3 : 3 3 : 1 3 : 1" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
318 <has_text text="2 | 2 2 | 2 2 | 3 2 | 3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
319 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
320 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
321 <output name="flow">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
322 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
323 <has_text text="6 (2,1) 5 (2,1) 4 (2,1) 3 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
324 <has_text text="E : A E : A G : C E : C" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
325 <has_text text="E | A E | A G | C E | C" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
326 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
327 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
328 <output name="errors">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
329 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
330 <has_text text="FAMILY PERSON MARKER RATIO" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
331 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
332 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
333 </test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
334 <test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
335 <!-- This test uses random optional parameter along with a conditional parameter. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
336 <param name="pname" value="basic2.ped"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
337 <param name="mname" value="basic2.map"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
338 <param name="dname" value="basic2.dat"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
339 <param name="allelefreq" value="individuals"/>
2
eae84c835026 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c4e0de9b6bb44d2d930f964f2a35a1cc940f59e0"
iuc
parents: 1
diff changeset
340 <param name="randomseed" value="5" />
1
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
341 <output name="merlinoutput">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
342 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
343 <has_text text= "Phenotype: some_disease [ALL] (1 family)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
344 <has_text text= "Pos Zmean pvalue delta LOD pvalue" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
345 <not_has_text text="--markerNames [ON]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
346 <not_has_text text="--minStep [2.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
347 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
348 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
349 <output name="chromosome">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
350 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
351 <has_text text="1 (F) 2 (F) 3 (F) 4 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
352 <has_text text="3 : 3 4 : 4 2 : 1 4 : 3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
353 <has_text text="2 : ? 2 : ? 2 : 2 2 | 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
354 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
355 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
356 <output name="flow">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
357 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
358 <has_text text="FAMILY 1 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
359 <has_text text="1 (F) 2 (F) 3 (F) 4 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
360 <has_text text="A : B C : D E : F C : A" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
361 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
362 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
363 <output name="errors">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
364 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
365 <has_text text="FAMILY PERSON MARKER RATIO" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
366 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
367 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
368 </test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
369 <test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
370 <!-- This test uses two optional parameters along with a conditional parameter. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
371 <param name="pname" value="error.ped"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
372 <param name="mname" value="error.map"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
373 <param name="dname" value="error.dat"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
374 <param name="allelefreq" value="equal"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
375 <param name="start" value="3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
376 <param name="markerNames" value="true" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
377 <output name="merlinoutput">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
378 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
379 <has_text text= "Family: 2 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
380 <has_text text= "Family: 73 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
381 <has_text text= "Family: 81 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
382 <has_text text= "Family: 94 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
383 <has_text text= "Family: 136 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
384 <has_text text= "Family: 162 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
385 <has_text text= "Family: 164 - Founders: 2 - Descendants: 2 - Bits: 2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
386 <has_text text= "--start [3.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
387 <has_text text="--markerNames [ON]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
388 <not_has_text text="--minStep [2.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
389 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
390 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
391 <output name="chromosome">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
392 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
393 <has_text text="FAMILY 200 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
394 <has_text text="1 (F) 2 (F) 4 (2,1) 3 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
395 <has_text text="4 : 1 4 : 1 4 : 4 1 : 1" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
396 <has_text text="3,4A : 3 4,3A : 3 4,3A | A3,4 3 | 3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
397 <has_text text="2,4A : B4,1 4,2A : B1,4 4,2A | A2,4 1,4B | B4,1" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
398 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
399 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
400 <output name="flow">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
401 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
402 <has_text text="FAMILY 200 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
403 <has_text text=" A : B C : D C : A D : B" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
404 <has_text text="A : B C : D C | A D | B" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
405 <has_text text="A : B C : D C | A D | B" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
406 <has_text text="A : B C : D C | A D \ A" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
407 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
408 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
409 <output name="errors">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
410 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
411 <has_text text="2 3 MRK11 0.00352" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
412 <has_text text="2 4 MRK11 0.00352" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
413 <has_text text="73 3 MRK17 0.00983" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
414 <has_text text="73 4 MRK17 0.00983" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
415 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
416 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
417 </test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
418 <test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
419 <!-- This test uses three optional parameters along with a conditional parameter. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
420 <param name="pname" value="gene.ped"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
421 <param name="mname" value="gene.map"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
422 <param name="dname" value="gene.dat"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
423 <param name="steps" value="3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
424 <param name="grid" value="2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
425 <param name="stop" value="4" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
426 <param name="randomseed" value="5" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
427 <param name="allelefreq" value="founders"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
428 <output name="merlinoutput">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
429 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
430 <has_text text= "SNP-1 SNP-2 SNP-3 SNP-4 SNP-5 SNP-6 SNP-7 SNP-8" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
431 <has_text text= "--stop [4.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
432 <has_text text= "--steps [3]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
433 <has_text text= "--grid [2.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
434 <not_has_text text="--markerNames [ON]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
435 <not_has_text text="--minStep [2.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
436 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
437 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
438 <output name="chromosome">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
439 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
440 <has_text text="FAMILY 12 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
441 <has_text text="1 (F) 2 (F) 3 (F) 4 (F)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
442 <has_text text="6 (4,3) 5 (2,1) 8 (6,5) 7 (6,5)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
443 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
444 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
445 <output name="flow">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
446 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
447 <has_text text="6 (4,3) 5 (2,1) 8 (6,5) 7 (6,5)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
448 <has_text text="G : E C : A G : A G : A" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
449 <has_text text="G | E C | A G | A G | A" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
450 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
451 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
452 <output name="errors">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
453 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
454 <has_text text="FAMILY PERSON MARKER RATIO" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
455 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
456 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
457 </test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
458 <test>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
459 <!-- This test uses all of the optional parameters along with a conditional paramter. -->
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
460 <param name="pname" value="snp-scan.ped"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
461 <param name="mname" value="snp-scan.map"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
462 <param name="dname" value="snp-scan.dat"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
463 <param name="markerNames" value="true" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
464 <param name="minStep" value="5" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
465 <param name="maxStep" value="6" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
466 <param name="steps" value="2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
467 <param name="allelefreq" value="equal"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
468 <param name="grid" value="4" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
469 <param name="start" value="2" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
470 <param name="stop" value="3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
471 <param name="randomseed" value="6" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
472 <output name="merlinoutput">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
473 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
474 <has_text text= "--markerNames [ON]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
475 <has_text text= "--minStep [5.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
476 <has_text text= "--maxStep [6.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
477 <has_text text= "--steps [2]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
478 <has_text text= "--grid [4.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
479 <has_text text= "--start [2.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
480 <has_text text= "--stop [3.00]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
481 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
482 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
483 <output name="chromosome">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
484 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
485 <has_text text= "FAMILY 500 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
486 <has_text text= "3,1A : A1,3 1,3A : A3,1 1,3A | A3,1 3,1A | A1,3" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
487 <has_text text= "4,1A : A1,4 1,4A : A4,1 1,4A | A4,1 4,1A | A1,4" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
488 <has_text text= "4,1A : A1,4 1,4A : A4,1 1,4A | A4,1 4,1A | A1,4" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
489 <has_text text= "1,3A : A3,1 3,1A : A1,3 3,1A | A1,3 1,3A | A3,1" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
490 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
491 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
492 <output name="flow">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
493 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
494 <has_text text= "FAMILY 500 [Most Likely]" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
495 <has_text text= " 1 (F) 2 (F) 5 (2,1) 4 (2,1)" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
496 <has_text text= " A : B C : D C : A D : B" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
497 <has_text text= "A : B C : D C | A D | B" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
498 <has_text text= "A : B C : D C | A D | B" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
499 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
500 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
501 <output name="errors">
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
502 <assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
503 <has_text text= "118 3 rs9510743 0.0239"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
504 <has_text text= "197 1 rs9580624 0.0230"/>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
505 <has_text text= "296 1 rs9510743 0.00914" />
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
506 </assert_contents>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
507 </output>
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
508 </test>
0
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
509 </tests>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
510 <help>
1
c88bc00301bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit 81594f752b46ed1ca0b6613e6db1de742f6425d1"
iuc
parents: 0
diff changeset
511 <![CDATA[ Finding disease genes using high-density single-nucleotide polymorphism (SNP) maps is a complicated task. By representing patterns of gene flow using sparse binary trees in general pedigrees using only the needed resources and then by deriving pedigree traversals algorithms, the likelihood calculations of the disease genes for the single marker or multi-marker can be carried out efficiently.
0
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513 `Multipoint Engine for Rapid Likelihood Inference (Merlin) is a computer program that ignores the unlikely possibility of a large number of recombinants on a multipoint calculation. This choice of Merlin increases the speed for pedigree analysis with accurate results.
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514 <http://csg.sph.umich.edu/abecasis/merlin/tour/linkage.html>`_
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516 `Merlin performs pedigree analysis by representing the gene flow in pedigrees using a sparse inheritance tree. It also performs rapid haplotyping, genotype error detection, and affected pair linkage analyses and can handle more markers than other pedigree analysis packages. <http://csg.sph.umich.edu/abecasis/merlin/tour/linkage.html>`_
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517
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518 Information:
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519 1. A pedigree is a genetic representation of a family tree that picturizes the inheritance of a trait or disease through several generations.
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520 2. Gene Flow is the transfer of genetic variation from one population to another.
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521 3. Sparse Tree: A two-dimensional matrix with m rows and n columns with most of its elements being zero.
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522 4. Haplotype: It is a combination of alleles or set of single nucleotide polymorphisms on the same chromosome is a set of DNA variations, or polymorphisms, that tend to be inherited together.
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523 5. Genotype Error: It occurs when the observed genotype of an individual does not correspond to the true genotype
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524 ]]>
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525 </help>
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526 <citations>
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527 <citation type="doi">10.1038/ng786</citation>
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528 <citation type="doi">10.1086/381652</citation>
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529 <citation type="doi">10.1002/gepi.20151</citation>
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530 <citation type="doi">10.1086/521580</citation>
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531 </citations>
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532 </tool>