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1 <tool id="flapjack_hdf52fj" name="HDF5 to Flapjack" version="0.0.1">
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2
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3 <description>convert an HDF5 formatted genotype file into a Flapjack-formatted genotype file</description>
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4 <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Hdf5ToFJTabbedConverter
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5 -hdf5=$hdf5
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6 -lines=$lines
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7 -markers=$markers
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8 -missing_filter=$missing_filter
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9 -heterozygous_filter=$heterozygous_filter
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10 -genotypes=$genotypes
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11 </command>
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12 <inputs>
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13 <param format="h5" name="hdf5" type="data" label="Source file"
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14 help="Flapjack's flavour of HDF5 for storing genotype data."/>
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15 <param format="txt" name="lines" type="data" label="Source file"
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16 help="A list of lines desired in the output. One line name per line on each line of the file."/>
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17 <param format="txt" name="markers" type="data" label="Source file"
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18 help="A list of markers desired in the output. One line name per marker on each line of the file."/>
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19 <param name="missing_filter" type="boolean" label="Filter out missing markers"
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20 truevalue="true" falsevalue="false">
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21 </param>
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22 <param name="heterozygous_filter" type="boolean" label="Filter out heterozygous markers"
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23 truevalue="true" falsevalue="false">
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24 </param>
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25 <param name="memory" type="select" label="Memory"
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26 help="How much memory to use; larger files may require more memory">
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27 <option selected="true" value="64m">64MB</option>
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28 <option value="128m">128MB</option>
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29 <option value="256m">256MB</option>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data format="fjgenotype" name="genotypes" />
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34 </outputs>
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35
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36 <help><![CDATA[
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37 .. class:: infomark
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38
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39 **What it does**
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40
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41 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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42 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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43
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44 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
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45 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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46
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47 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
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48
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49
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50
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51 ]]></help>
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52 <citations>
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53 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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54 </citations>
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55 </tool> |
