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comparison cropgeeks_flapjack/flapjack.xml @ 0:830715268b52 draft default tip

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author cropgeeks
date Tue, 14 Feb 2017 06:30:51 -0500
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1 <tool id="jhi_flapjack" name="Flapjack to HDF5" version="0.0.1">
2 <description>convert a Flapjack-formatted genotype file into HDF5</description>
3 <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter -genotypes=$input_genotypes -hdf5=$output_hdf5</command>
4 <inputs>
5 <param format="csv,tabular,txt" name="input_genotypes" type="data" label="Source file"
6 help="====Flapjack-formatted (tab-delimited text) input file of genotype data"/>
7 <param name="memory" type="select" label="Memory"
8 help="How much memory to use; larger files may require more memory">
9 <option selected="true" value="64m">64MB</option>
10 <option value="128m">128MB</option>
11 <option value="256m">256MB</option>
12 </param>
13 </inputs>
14 <outputs>
15 <data format="h5" name="output_hdf5" />
16 </outputs>
17
18 <help><![CDATA[
19 .. class:: infomark
20
21 **What it does**
22
23 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
24 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
25
26 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
27 See Flapjack's documentation_ for more details on the various Flapjack data formats.
28
29 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
30
31
32
33 ]]></help>
34 <citations>
35 <citation type="doi">10.1093/bioinformatics/btq580</citation>
36 </citations>
37 </tool>