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annotate fj2hdf5.xml @ 73:c79e832868ed draft

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author cropgeeks
date Thu, 22 Feb 2018 10:15:09 -0500
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1 <tool id="flapjack_fj2hdf5" 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><![CDATA[
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4 java
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5 #if $adv_opts.show_advanced
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6 -Xmx$adv_opts.memory
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7 #end if
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8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter
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9 -g $genotypes
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10 -h $output
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11 ]]></command>
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12 <inputs>
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13 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
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14 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
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15
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16 <conditional name="adv_opts">
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17 <param name="show_advanced" type="boolean"
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18 label="Enable advanced options"
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19 truevalue="show" falsevalue="">
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20 </param>
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21 <when value="show">
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22 <param name="memory" type="select"
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23 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 </when>
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30 </conditional>
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31 </inputs>
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32
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33 <outputs>
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34 <data format="h5" name="output" />
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35 </outputs>
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36
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37 <stdio>
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38 <exit_code range="1:" />
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39 </stdio>
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40
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41 <help><![CDATA[
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42 .. class:: infomark
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43
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44 **What it does**
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45
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46 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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47 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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48
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49 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
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50 See Flapjack's documentation_ for more details on the various Flapjack data formats.
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51
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52 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
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53 ]]></help>
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54
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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>