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1 <tool id="jhi_flapjack" name="Flapjack to HDF5" version="0.0.1">
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2 <description>convert a Flapjack-formatted genotype file into HDF5</description>
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3 <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter -genotypes=$input_genotypes -hdf5=$output_hdf5</command>
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4 <inputs>
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5 <param format="csv,tabular,txt" name="input_genotypes" type="data" label="Source file"
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6 help="====Flapjack-formatted (tab-delimited text) input file of genotype data"/>
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7 <param name="memory" type="select" label="Memory"
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8 help="How much memory to use; larger files may require more memory">
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9 <option selected="true" value="64m">64MB</option>
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10 <option value="128m">128MB</option>
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11 <option value="256m">256MB</option>
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12 </param>
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13 </inputs>
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14 <outputs>
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15 <data format="h5" name="output_hdf5" />
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16 </outputs>
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17
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18 <help><![CDATA[
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19 .. class:: infomark
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20
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21 **What it does**
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22
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23 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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24 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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25
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26 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
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27 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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28
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29 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
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30
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31
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32
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33 ]]></help>
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34 <citations>
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35 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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36 </citations>
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37 </tool> |
