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1 <tool id="flapjack_split_by_sample" name="Flapjack Split By Sample" version="0.0.1">
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2 <description>create a Flapjack project file from Flapjack formatted input files.</description>
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72
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3 <requirements>
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4 <requirement type="package" version="0.14.1">pandas</requirement>
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5 </requirements>
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6 <command>
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7 python $__tool_directory__/FlapjackProject.py
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8 -j $__tool_directory__/lib/flapjack.jar
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9 -J $__tool_directory__/lib/pedigreeheader.jar
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10 -g '$genotypes'
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11 -s '$traits'
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12 -p '$output'
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13 #if $map
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14 -m '$map'
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15 #end if
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16 #if $qtls
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17 -q '$qtls'
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18 #end if
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19 #if $adv_opts.show_advanced
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20 -M "$adv_opts.missingData"
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21 -S "$adv_opts.hetSep"
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22 #end if
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23 </command>
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24 <inputs>
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25 <param format="fjgenotype, tabular, text" name="genotypes" type="data" label="Flapjack genotype file"
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26 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
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27
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28 <param format="tabular, text" name="traits" type="data" label="Flapjack phenotype file"
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29 help="Flapjack-formatted (tab-delimited text) input file of phenotype data"/>
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30
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31 <param format="fjmap, tabular, text" name="map" type="data" label="Flapjack map file"
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32 help="Flapjack-formatted (tab-delimited text) input file of map data"
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33 optional="true"/>
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34
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35 <param format="fjqtl, tabular, text" name="qtls" type="data" label="Flapjack QTL file"
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36 help="Flapjack-formatted (tab-delimited text) input file of QTL data"
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37 optional="true"/>
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38
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39 <!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
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40 <conditional name="adv_opts">
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41 <param name="show_advanced" type="boolean"
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42 label="Enable advanced options"
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43 truevalue="show" falsevalue="">
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44 </param>
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45 <when value="show">
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46 <param name="missingData" type="text" value="-"
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47 label="Missing data string"
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48 help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
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49
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50 <param name="hetSep" type="text" value="/"
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51 label="Heterozygous allele separator string"
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52 help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
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53 </when>
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54 </conditional>
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55 <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
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56 </inputs>
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57
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58 <outputs>
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59 <data name="output" format="flapjack" />
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60 </outputs>
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61
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62 <stdio>
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63 <exit_code range="1:" />
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64 </stdio>
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65
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66 <help><![CDATA[
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67 .. class:: infomark
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68
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69 **What it does**
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70
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71 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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72 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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73
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74 This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files.
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75 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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76 More information on the CreateProject tool can be found here_
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77
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78 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
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79 .. _here: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#createproject-exe-jhi-flapjack-io-createproject
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80 ]]></help>
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81
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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> |
