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