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1 <tool id="flapjack_hapmap2fj" name="HapMap to Flapjack" version="0.0.1">
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2
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3 <!--System.out.println("Usage: hapmap2flapjack <options>\n"
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4 + " where valid options are:\n"
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5 + " -separator=<s or t> (required separator used in input file)\n"
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6 + " -hapmap=<hapmap_file> (required input file)\n"
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7 + " -map=<map_file> (required output file)\n"
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8 + " -genotypes=<genotype_file> (required output file)\n");-->
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9
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10 <description>convert an HapMap formatted file into a Flapjack-formatted genotype file</description>
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11 <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.HapMapToFJTabbedConverter
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12 -hapmap=$hapmap
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13 -separator=$separator
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14 -map=$map
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15 -genotypes=$genotypes
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16 </command>
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17 <inputs>
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18 <param format="txt" name="hapmap" type="data" label="Source file"
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19 help="HapMap Formatted File"/>
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20 <param name="separator" type="boolean" label="File is tab-separated"
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21 truevalue="t" falsevalue="s">
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22 </param>
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23 <param name="memory" type="select" label="Memory"
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24 help="How much memory to use; larger files may require more memory">
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25 <option selected="true" value="64m">64MB</option>
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26 <option value="128m">128MB</option>
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27 <option value="256m">256MB</option>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data format="fjmap" name="map" />
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32 <data format="fjgenotype" name="genotypes" />
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33 </outputs>
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34
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35 <stdio>
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36 <exit_code range="1:" />
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37 </stdio>
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38
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39 <help><![CDATA[
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40 .. class:: infomark
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41
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42 **What it does**
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43
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44 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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45 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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46
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47 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
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48 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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49
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50 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
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51
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52
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53
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54 ]]></help>
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55 <citations>
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56 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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57 </citations>
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58 </tool> |
