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annotate merlin.xml @ 0:625146aa31d8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
author iuc
date Thu, 07 May 2020 13:54:14 -0400
parents
children c88bc00301bf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
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1 <?xml version="1.0" encoding="utf-8"?>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
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2 <tool id="merlin" name="Tool for Linkage Analysis" version="1.1.2.1">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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3 <requirements>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
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4 <requirement type="package" version="1.1.2">merlin</requirement>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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5 </requirements>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
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6 <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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7 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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8
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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9 #if $minStep
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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10 --minStep '$minStep'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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11 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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12
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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13 #if $maxStep
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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14 --maxStep '$maxStep'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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15 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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16
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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17 #if $steps
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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18 --steps '$steps'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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19 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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20
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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21 #if $grid
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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22 --grid '$grid'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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23 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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24
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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25 #if $start
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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26 --start '$start'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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27 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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28
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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29 #if $stop
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30 --stop '$stop'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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31 #end if
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32
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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33 #if $randomseed
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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34 -r '$randomseed'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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35 #end if
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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36
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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37 #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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38 -fm
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
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39 #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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40 -ff
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
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41 #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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42 -fa
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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43 #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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44 -fe
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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45 #elif $allelefrequency.allelefreq.value == "file":
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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46 -f '$allelefrequency.file'
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47 #end if
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48
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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49 > '$merlinoutput'
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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50 ]]></command>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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51 <inputs>
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52 <!-- Select input data file -->
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53 <param name="pname" type="data" format="txt" label="Entering Data File" help="Selects input data file, in linkage or QTDT format" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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54 <!-- Select input map file -->
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55 <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." />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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56 <!-- Select input pedigree file -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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57 <param name="dname" type="data" format="txt" label="Entering Pedigree File" help="Selects pedigree file, with genotype, phenotype and family structure information" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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58 <!-- Beginning of the optional parameters -->
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59 <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." />
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60 <param name="minStep" type="float" optional="true" label="For Minimum Step Optional Parameter" help="Useful to find the minimum value" />
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61 <param name="maxStep" type="float" optional="true" label="For Maximum Step Optional Paramter" help="Useful to find the maximum value" />
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62 <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" />
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63 <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" />
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64 <param name="start" type="integer" min="0" optional="true" label="Start analyses" help="Start analyses at pos centiMorgans." />
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65 <param name="stop" type="integer" min="0" optional="true" label="Stop analyses" help="Stop analyses at pos centiMorgans." />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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66 <param name="randomseed" type="integer" min="0" optional="true" label="Random Sequence" help="Selects a different random sequence for simulation and sampling of haplotypes." />
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67 <!-- Beginning of the conditional parameters -->
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68 <conditional name="allelefrequency">
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69 <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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70 <option value="maxlike"> Maximum Likelihood </option>
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71 <option value="founders"> Founders </option>
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72 <option value="individuals">All Individuals</option>
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73 <option value="equal">Assume Equal</option>
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74 <option value="file">User File</option>
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75 </param>
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76 <when value="maxlike">
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77 <!-- Nothing to be added. -->
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78 </when>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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79 <when value="founders">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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80 <!-- Nothing to be added. -->
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81 </when>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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82 <when value="individuals">
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83 <!-- Nothing to be added. -->
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84 </when>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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85 <when value="equal">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
86 <!-- Nothing to be added. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
87 </when>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
88 <when value="file">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
89 <param name="file" type="data" format="tabular" label="User Specified file for Allele frequencies" help="Source for allele frequency information."/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
90 </when>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
91 </conditional>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
92 </inputs>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
93 <outputs>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
94 <!-- Set of outputs along with the formats. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
95 <data name="errors" format="txt" from_work_dir="merlin.err" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
96 <data name="flow" format="txt" from_work_dir="merlin.flow" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
97 <data name="chromosome" format="txt" from_work_dir="merlin.chr" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
98 <data name="merlinoutput" format="lod" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
99 </outputs>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
100 <tests>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
101 <test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
102 <!-- No optional parameters used in this test but testing a conditional parameter and random value. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
103 <param name="pname" value="parametric.ped"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
104 <param name="mname" value="parametric.map"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
105 <param name="dname" value="parametric.dat"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
106 <param name="allelefreq" value="file"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
107 <param name="file" value="alle.txt" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
108 <param name="randomseed" value="2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
109 <output name="merlinoutput">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
110 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
111 <has_text text="MRK1 MRK2 MRK3 MRK4 MRK5 MRK6 MRK7 MRK8 MRK9 MRK10" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
112 <not_has_text text="--minStep [2]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
113 <has_line line="Phenotype: VERY_RARE_DISEASE [ALL] (1 family)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
114 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
115 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
116 <output name="chromosome">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
117 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
118 <has_text text="FAMILY 1 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
119 <has_text text="208 (F) 207 (102,101) 305 (208,207) 202 (102,101)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
120 <has_text text="4 : 1 4 : 1 3 : 3 3 : 3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
121 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
122 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
123 <output name="flow">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
124 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
125 <has_text text="FAMILY 1 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
126 <has_text text="101 (F) 102 (F) 201 (F) 203 (F)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
127 <has_text text="A : B C : D E : F G : H" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
128 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
129 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
130 <output name="errors">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
131 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
132 <has_text text="FAMILY PERSON MARKER RATIO" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
133 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
134 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
135 </test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
136 <test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
137 <!-- This test uses markerNames optional parameter and maxlike option in this test case leads to error. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
138 <param name="pname" value="x.ped"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
139 <param name="mname" value="x.map"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
140 <param name="dname" value="x.dat"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
141 <param name="markerNames" value="true" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
142 <!-- Selecting allele frequency can be estimated by counting in founders. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
143 <param name="allelefreq" value="founders"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
144 <param name="randomseed" value="6" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
145 <output name="merlinoutput">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
146 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
147 <has_text text= "MRK1 MRK2 MRK3 MRK4 MRK5 MRK6 MRK7 MRK8 MRK9 MRK10" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
148 <has_text text= "Family: 1 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
149 <has_text text="Family: 2 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
150 <has_text text= "Family: 3 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
151 <has_text text= "Family: 4 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
152 <has_text text= "Family: 5 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
153 <not_has_text text="--minStep [2]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
154 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
155 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
156 <output name="chromosome">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
157 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
158 <has_text text="FAMILY 5 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
159 <has_text text="1 (F) 2 (F) 4 (2,1) 3 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
160 <has_text text="2 : 2 4 : 2 4 : 2 2 : 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
161 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
162 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
163 <output name="flow">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
164 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
165 <has_text text="FAMILY 5 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
166 <has_text text="1 (F) 2 (F) 4 (2,1) 3 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
167 <has_text text="A : B C : D C : A D : A" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
168 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
169 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
170 <output name="errors">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
171 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
172 <has_text text="FAMILY PERSON MARKER RATIO" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
173 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
174 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
175 </test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
176 <test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
177 <!-- This test uses minStep optional parameter -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
178 <param name="pname" value="haplo.ped"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
179 <param name="mname" value="haplo.map"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
180 <param name="dname" value="haplo.dat"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
181 <!-- Selecting allele frequency can be estimated by counting in all individuals. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
182 <param name="allelefreq" value="individuals"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
183 <param name="minStep" value="2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
184 <param name="randomseed" value="5" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
185 <output name="merlinoutput">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
186 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
187 <has_text text= "SNP-1 SNP-2 SNP-3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
188 <has_text text= "--minStep [2.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
189 <not_has_text text="--markerNames [ON]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
190 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
191 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
192 <output name="chromosome">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
193 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
194 <has_text text="FAMILY 3 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
195 <has_text text="1 (F) 2 (F) 3 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
196 <has_text text="1,2A : A2,1 2,1A : A1,2 2,1A | A1,2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
197 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
198 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
199 <output name="flow">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
200 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
201 <has_text text="FAMILY 3 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
202 <has_text text="1 (F) 2 (F) 3 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
203 <has_text text="A : B C : D C : A" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
204 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
205 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
206 <output name="errors">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
207 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
208 <has_text text="FAMILY PERSON MARKER RATIO" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
209 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
210 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
211 </test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
212 <test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
213 <!--This test uses steps optinal parameter -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
214 <param name="pname" value="asp.ped"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
215 <param name="mname" value="asp.map"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
216 <param name="dname" value="asp.dat"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
217 <!-- Selecting allele frequency can be estimated by assuming equal allele frequencies. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
218 <param name="allelefreq" value="equal"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
219 <param name="steps" value="3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
220 <output name="merlinoutput">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
221 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
222 <has_text text= "Phenotype: affection [ALL] (200 families)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
223 <has_text text= "--steps [3]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
224 <not_has_text text="--markerNames [ON]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
225 <not_has_text text="--minStep [2.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
226 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
227 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
228 <output name="chromosome">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
229 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
230 <has_text text= "FAMILY 200 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
231 <has_text text= "1 (F) 2 (F) 4 (2,1) 3 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
232 <has_text text= "4 : 1 4 : 1 4 : 4 1 : 1" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
233 <has_text text=" 3,4A : 3 4,3A : 3 4,3A | A3,4 3 | 3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
234 <has_text text="2,4A : B4,1 4,2A : B1,4 4,2A | A2,4 1,4B | B4,1" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
235 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
236 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
237 <output name="flow">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
238 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
239 <has_text text= "FAMILY 200 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
240 <has_text text= "1 (F) 2 (F) 4 (2,1) 3 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
241 <has_text text= "A : B C : D C : A C : A" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
242 <has_text text="A : B C : D C | A C | A" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
243 <has_text text="A : B C : D C | A C | A" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
244 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
245 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
246 <output name="errors">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
247 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
248 <has_text text="FAMILY PERSON MARKER RATIO" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
249 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
250 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
251 </test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
252 <test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
253 <!-- This test uses grid optional parameter -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
254 <param name="pname" value="sibs.ped"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
255 <param name="mname" value="sibs.map"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
256 <param name="dname" value="sibs.dat"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
257 <param name="allelefreq" value="maxlike"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
258 <param name="grid" value="3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
259 <output name="merlinoutput">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
260 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
261 <has_text text= "SNP_1 SNP_2 SNP_3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
262 <has_text text= "Family: 29 - Founders: 2 - Descendants: 4 - Bits: 6" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
263 <has_text text= "--grid [3.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
264 <not_has_text text="--markerNames [ON]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
265 <not_has_text text="--minStep [2.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
266 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
267 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
268 <output name="chromosome">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
269 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
270 <has_text text="FAMILY 50 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
271 <has_text text="1 (F) 2 (F) 6 (2,1) 5 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
272 <has_text text="2 : 2 1 : 2 1 : 2 2 : 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
273 <has_text text="2 : 1 1 : 1 1 | 2 1 | 1" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
274 <has_text text="2 : 1 1 : 1 1 | 2 1 | 1" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
275 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
276 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
277 <output name="flow">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
278 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
279 <has_text text="FAMILY 50 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
280 <has_text text="1 (F) 2 (F) 6 (2,1) 5 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
281 <has_text text="A : B C : D C : A C : B" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
282 <has_text text="A : B C : D C | A C | B" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
283 <has_text text="A : B C : D C | A C | B" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
284 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
285 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
286 <output name="errors">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
287 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
288 <has_text text="29 4 SNP_1" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
289 <has_text text="29 4 SNP_3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
290 <has_text text="29 5 SNP_3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
291 <has_text text="29 6 SNP_3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
292 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
293 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
294 </test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
295 <test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
296 <!-- This test uses start optional parameter along with a conditional parameter -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
297 <param name="pname" value="assoc.ped"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
298 <param name="mname" value="assoc.map"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
299 <param name="dname" value="assoc.dat"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
300 <param name="allelefreq" value="founders"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
301 <param name="start" value="2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
302 <output name="merlinoutput">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
303 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
304 <has_text text= "--start [2.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
305 <not_has_text text="--markerNames [ON]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
306 <not_has_text text="--minStep [2.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
307 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
308 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
309 <output name="chromosome">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
310 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
311 <has_text text="6 (2,1) 5 (2,1) 4 (2,1) 3 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
312 <has_text text="3 : 3 3 : 3 3 : 1 3 : 1" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
313 <has_text text="2 | 2 2 | 2 2 | 3 2 | 3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
314 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
315 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
316 <output name="flow">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
317 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
318 <has_text text="6 (2,1) 5 (2,1) 4 (2,1) 3 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
319 <has_text text="E : A E : A G : C E : C" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
320 <has_text text="E | A E | A G | C E | C" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
321 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
322 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
323 <output name="errors">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
324 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
325 <has_text text="FAMILY PERSON MARKER RATIO" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
326 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
327 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
328 </test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
329 <test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
330 <!-- This test uses random optional parameter along with a conditional parameter. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
331 <param name="pname" value="basic2.ped"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
332 <param name="mname" value="basic2.map"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
333 <param name="dname" value="basic2.dat"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
334 <param name="allelefreq" value="individuals"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
335 <param name="random" value="5" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
336 <output name="merlinoutput">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
337 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
338 <has_text text= "Phenotype: some_disease [ALL] (1 family)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
339 <has_text text= "Pos Zmean pvalue delta LOD pvalue" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
340 <not_has_text text="--markerNames [ON]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
341 <not_has_text text="--minStep [2.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
342 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
343 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
344 <output name="chromosome">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
345 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
346 <has_text text="1 (F) 2 (F) 3 (F) 4 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
347 <has_text text="3 : 3 4 : 4 2 : 1 4 : 3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
348 <has_text text="2 : ? 2 : ? 2 : 2 2 | 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
349 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
350 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
351 <output name="flow">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
352 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
353 <has_text text="FAMILY 1 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
354 <has_text text="1 (F) 2 (F) 3 (F) 4 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
355 <has_text text="A : B C : D E : F C : A" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
356 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
357 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
358 <output name="errors">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
359 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
360 <has_text text="FAMILY PERSON MARKER RATIO" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
361 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
362 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
363 </test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
364 <test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
365 <!-- This test uses two optional parameters along with a conditional parameter. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
366 <param name="pname" value="error.ped"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
367 <param name="mname" value="error.map"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
368 <param name="dname" value="error.dat"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
369 <param name="allelefreq" value="equal"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
370 <param name="start" value="3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
371 <param name="markerNames" value="true" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
372 <output name="merlinoutput">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
373 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
374 <has_text text= "Family: 2 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
375 <has_text text= "Family: 73 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
376 <has_text text= "Family: 81 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
377 <has_text text= "Family: 94 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
378 <has_text text= "Family: 136 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
379 <has_text text= "Family: 162 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
380 <has_text text= "Family: 164 - Founders: 2 - Descendants: 2 - Bits: 2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
381 <has_text text= "--start [3.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
382 <has_text text="--markerNames [ON]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
383 <not_has_text text="--minStep [2.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
384 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
385 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
386 <output name="chromosome">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
387 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
388 <has_text text="FAMILY 200 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
389 <has_text text="1 (F) 2 (F) 4 (2,1) 3 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
390 <has_text text="4 : 1 4 : 1 4 : 4 1 : 1" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
391 <has_text text="3,4A : 3 4,3A : 3 4,3A | A3,4 3 | 3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
392 <has_text text="2,4A : B4,1 4,2A : B1,4 4,2A | A2,4 1,4B | B4,1" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
393 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
394 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
395 <output name="flow">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
396 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
397 <has_text text="FAMILY 200 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
398 <has_text text=" A : B C : D C : A D : B" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
399 <has_text text="A : B C : D C | A D | B" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
400 <has_text text="A : B C : D C | A D | B" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
401 <has_text text="A : B C : D C | A D \ A" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
402 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
403 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
404 <output name="errors">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
405 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
406 <has_text text="2 3 MRK11 0.00352" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
407 <has_text text="2 4 MRK11 0.00352" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
408 <has_text text="73 3 MRK17 0.00983" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
409 <has_text text="73 4 MRK17 0.00983" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
410 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
411 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
412 </test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
413 <test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
414 <!-- This test uses three optional parameters along with a conditional parameter. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
415 <param name="pname" value="gene.ped"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
416 <param name="mname" value="gene.map"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
417 <param name="dname" value="gene.dat"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
418 <param name="steps" value="3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
419 <param name="grid" value="2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
420 <param name="stop" value="4" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
421 <param name="randomseed" value="5" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
422 <param name="allelefreq" value="founders"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
423 <output name="merlinoutput">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
424 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
425 <has_text text= "SNP-1 SNP-2 SNP-3 SNP-4 SNP-5 SNP-6 SNP-7 SNP-8" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
426 <has_text text= "--stop [4.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
427 <has_text text= "--steps [3]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
428 <has_text text= "--grid [2.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
429 <not_has_text text="--markerNames [ON]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
430 <not_has_text text="--minStep [2.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
431 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
432 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
433 <output name="chromosome">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
434 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
435 <has_text text="FAMILY 12 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
436 <has_text text="1 (F) 2 (F) 3 (F) 4 (F)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
437 <has_text text="6 (4,3) 5 (2,1) 8 (6,5) 7 (6,5)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
438 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
439 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
440 <output name="flow">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
441 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
442 <has_text text="6 (4,3) 5 (2,1) 8 (6,5) 7 (6,5)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
443 <has_text text="G : E C : A G : A G : A" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
444 <has_text text="G | E C | A G | A G | A" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
445 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
446 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
447 <output name="errors">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
448 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
449 <has_text text="FAMILY PERSON MARKER RATIO" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
450 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
451 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
452 </test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
453 <test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
454 <!-- This test uses all of the optional parameters along with a conditional paramter. -->
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
455 <param name="pname" value="snp-scan.ped"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
456 <param name="mname" value="snp-scan.map"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
457 <param name="dname" value="snp-scan.dat"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
458 <param name="markerNames" value="true" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
459 <param name="minStep" value="5" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
460 <param name="maxStep" value="6" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
461 <param name="steps" value="2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
462 <param name="allelefreq" value="equal"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
463 <param name="grid" value="4" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
464 <param name="start" value="2" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
465 <param name="stop" value="3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
466 <param name="randomseed" value="6" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
467 <output name="merlinoutput">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
468 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
469 <has_text text= "--markerNames [ON]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
470 <has_text text= "--minStep [5.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
471 <has_text text= "--maxStep [6.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
472 <has_text text= "--steps [2]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
473 <has_text text= "--grid [4.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
474 <has_text text= "--start [2.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
475 <has_text text= "--stop [3.00]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
476 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
477 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
478 <output name="chromosome">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
479 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
480 <has_text text= "FAMILY 500 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
481 <has_text text= "3,1A : A1,3 1,3A : A3,1 1,3A | A3,1 3,1A | A1,3" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
482 <has_text text= "4,1A : A1,4 1,4A : A4,1 1,4A | A4,1 4,1A | A1,4" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
483 <has_text text= "4,1A : A1,4 1,4A : A4,1 1,4A | A4,1 4,1A | A1,4" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
484 <has_text text= "1,3A : A3,1 3,1A : A1,3 3,1A | A1,3 1,3A | A3,1" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
485 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
486 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
487 <output name="flow">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
488 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
489 <has_text text= "FAMILY 500 [Most Likely]" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
490 <has_text text= " 1 (F) 2 (F) 5 (2,1) 4 (2,1)" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
491 <has_text text= " A : B C : D C : A D : B" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
492 <has_text text= "A : B C : D C | A D | B" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
493 <has_text text= "A : B C : D C | A D | B" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
494 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
495 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
496 <output name="errors">
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
497 <assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
498 <has_text text= "118 3 rs9510743 0.0239"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
499 <has_text text= "197 1 rs9580624 0.0230"/>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
500 <has_text text= "296 1 rs9510743 0.00914" />
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
501 </assert_contents>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
502 </output>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
503 </test>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
504 </tests>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
505 <help>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
506 <![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.
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
507
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
508 `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.
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
509 <http://csg.sph.umich.edu/abecasis/merlin/tour/linkage.html>`_
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
510
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
511 `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>`_
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
512
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
513 Information:
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
parents:
diff changeset
514 1. A pedigree is a genetic representation of a family tree that picturizes the inheritance of a trait or disease through several generations.
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
iuc
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515 2. Gene Flow is the transfer of genetic variation from one population to another.
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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516 3. Sparse Tree: A two-dimensional matrix with m rows and n columns with most of its elements being zero.
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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517 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.
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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518 5. Genotype Error: It occurs when the observed genotype of an individual does not correspond to the true genotype
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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519 ]]>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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520 </help>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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521 <citations>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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522 <citation type="doi">10.1038/ng786</citation>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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523 <citation type="doi">10.1086/381652</citation>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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524 <citation type="doi">10.1002/gepi.20151</citation>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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525 <citation type="doi">10.1086/521580</citation>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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526 </citations>
625146aa31d8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ commit c472d8a5d535aab903e4a13e7b0c076ef1544c34"
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527 </tool>