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1 <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">
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2
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3 <!--System.out.println("Usage: createproject <options>\n"
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4 + " where valid options are:\n"
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5 + " -map=<map_file> (optional input file)\n"
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6 + " -genotypes=<genotypes_file> (required input file)\n"
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7 + " -traits=<traits_file> (optional input file)\n"
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8 + " -qtls=<qtl_file> (optional input file)\n"
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9 + " -decimalEnglish (optional input parameter)\n"
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10 + " -project=<project_file> (required output file)\n");-->
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11
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12 <description>Run pedigree verification of F1s (known parents) analysis</description>
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13 <command><![CDATA[
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14 java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject
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15 -map=$map -genotypes=$genotypes -galaxyHTML=$html -project=$output
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param format="fjmap" name="map" type="data" label="Flapjack map file"
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20 help="Flapjack-formatted (tab-delimited text) input file of map data"/>
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21 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
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22 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
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23
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24 <param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
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25 label="Read input data using decimal English"
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26 help="Build the index using a perfect hash rather than a dense hash. This will require less memory
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27 (especially during quantification), but will take longer to construct "/>
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28 <param name="memory" type="select" label="Memory"
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29 help="How much memory to use; larger files may require more memory">
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30 <option selected="true" value="64m">64MB</option>
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31 <option value="128m">128MB</option>
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32 <option value="256m">256MB</option>
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33 </param>
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34 </inputs>
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35 <outputs>
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5
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36 <!-- label="${tool.name} on ${on_string}: project.flapjack" -->
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37 <data name="output" format="flapjack" />
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38 <data name="html" format="html" />
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39 </outputs>
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40
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41 <stdio>
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42 <exit_code range="1:" />
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43 </stdio>
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44
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45 <help><![CDATA[
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46 .. class:: infomark
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47
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48 **What it does**
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49
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50 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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51 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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52
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53 This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files.
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54 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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55
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56 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
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57
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58
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59
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60 ]]></help>
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61 <citations>
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62 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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63 </citations>
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64 </tool> |
