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1 <tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1">
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2
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3 <description>Run marker assisted backcrossing analysis on a dataset</description>
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4
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5 <command><![CDATA[
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6 java
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7 #if $advanced_options.show_advanced
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8 -Xmx$advanced_options.memory
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9 #end if
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10 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
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51
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11 -m $map
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12 -g $genotypes
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13 -q $qtls
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14 -r $parent1
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15 -d $parent2
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16 -model $model
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52
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17 -c $coverage
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4
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18 #if $advanced_options.show_advanced
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19 $advanced_options.decimalEnglish
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20 #end if
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51
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21 -o $output
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22 #if $create_project
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23 -p $project
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43
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24 #end if
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25 ]]></command>
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26
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27 <inputs>
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28 <param format="fjmap" name="map" type="data" label="Flapjack map file"
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29 help="Flapjack-formatted (tab-delimited text) input file of map data"/>
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30 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
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31 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
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32 <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
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33 help="Flapjack-formatted (tab-delimited text) input file of QTL data"/>
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34 <param name="parent1" type="integer" value="1" label="Index of recurrent parent"
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35 help="The index of the recurrent parent in the genotype file"/>
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36 <param name="parent2" type="integer" value="2" label="Index of donor parent"
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37 help="The index of the donor parent in the genotype file"/>
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38 <param name="model" type="select" label="Model"
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39 help="The model to use for calculating statistics">
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40 <option selected="true" value="weighted">Weighted</option>
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41 <option value="unweighted">Unweighted</option>
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42 </param>
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43 <param name="coverage" type="float" value="10" label="Maximum coverage of a marker"
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44 help="The maximum length of genome a marker can represent"/>
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45 <conditional name="advanced_options">
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46 <param name="show_advanced" type="boolean" label="Enable advanced options"
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47 truevalue="show" falsevalue="">
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48 </param>
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49 <when value="show">
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51
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50 <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="True"
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4
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51 label="Force English-style decimal marks"
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52 help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy's locale settings"/>
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53 <param name="memory" type="select" label="Memory"
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54 help="How much memory to use; larger files may require more memory">
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55 <option selected="true" value="64m">64MB</option>
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56 <option value="128m">128MB</option>
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57 <option value="256m">256MB</option>
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58 </param>
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59 </when>
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43
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60 </conditional>
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61
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50
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62 <param name="create_project" type="boolean" label="Also create Flapjack project file"
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46
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63 truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results.">
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64 </param>
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65 </inputs>
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66
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67 <outputs>
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68 <data format="tabular" name="output" />
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43
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69 <data format="flapjack" name="project">
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50
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70 <filter>create_project</filter>
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43
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71 </data>
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72
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4
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73 </outputs>
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74
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75 <stdio>
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76 <exit_code range="1:" />
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77 </stdio>
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78
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79 <help><![CDATA[
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80 .. class:: infomark
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81
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82 **What it does**
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83
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84 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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85 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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86
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87 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
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88 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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89
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90 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
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91
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92 ]]></help>
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93 <citations>
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94 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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95 </citations>
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96 </tool> |
