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1 <tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1">
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2
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3 <!--System.out.println("Usage: pedverf1sstats <options>\n"
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4 + " where valid options are:\n"
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5 + " -map=<map_file> (required input file)\n"
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6 + " -genotypes=<genotypes_file> (required input file)\n"
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7 + " -parent1=<index_of_line> (required parameter, first line is index 1)\n"
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8 + " -parent2=<index_of_line> (required parameter, first line is index 1)\n"
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9 + " -expectedf1=<index_of_line> (optional parameter, first line is index 1)\n"
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10 + " -decimalEnglish (optional parameter)\n"
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11 + " -output=<output_file> (required output file)\n");-->
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12
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13 <description>Run pedigree verification of F1s (known parents) analysis</description>
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14 <command><![CDATA[
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15 java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats
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16 -map=$map -genotypes=$genotypes -parent1=$parent1 -parent2=$parent2
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17 #if $simulate_f1.simulate_f1_selector == "file":
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18 -expectedf1=$simulate_f1.expectedF1
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19 #end if
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20 $decimalEnglish -output=$output
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21 ]]>
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22 </command>
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23 <inputs>
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41
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24 <param format="fjmap" name="map" type="data" label="Flapjack map file"
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25 help="Flapjack-formatted (tab-delimited text) input file of map data"/>
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41
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26 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
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27 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
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28 <param name="parent1" type="integer" value="1" label="Index of parent 1"
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29 help="The index of the first parent in the genotype file"/>
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30 <param name="parent2" type="integer" value="2" label="Index of parent 2"
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31 help="The index of the second parent in the genotype file"/>
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32
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33 <conditional name="simulate_f1">
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34 <param name="simulate_f1_selector" type="select" label="Simulate expected F1 (or use F1 from file)">
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35 <option value="simulate" selected="True">Simulate</option>
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36 <option value="file">Select from file</option>
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37 </param>
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38 <when value="file">
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39 <param argument="-expectedF1" type="integer" value="3" label="Index of expected F1"
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40 help="The index of the donor parent in the genotype file"/>
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41 </when>
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42 </conditional>
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43
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44 <param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
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45 label="Read input data using decimal English"
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46 help="Build the index using a perfect hash rather than a dense hash. This will require less memory
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47 (especially during quantification), but will take longer to construct "/>
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48 <param name="memory" type="select" label="Memory"
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49 help="How much memory to use; larger files may require more memory">
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50 <option selected="true" value="64m">64MB</option>
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51 <option value="128m">128MB</option>
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52 <option value="256m">256MB</option>
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53 </param>
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54 </inputs>
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55 <outputs>
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56 <data format="tabular" name="output" />
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57 </outputs>
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58
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59 <stdio>
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60 <exit_code range="1:" />
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61 </stdio>
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62
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63 <help><![CDATA[
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64 .. class:: infomark
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65
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66 **What it does**
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67
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68 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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69 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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70
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71 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
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72 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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73
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74 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
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75
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76
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77
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78 ]]></help>
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79 <citations>
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80 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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81 </citations>
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82 </tool> |
