Mercurial > repos > cropgeeks > cropgeeks
comparison cropgeeks_flapjack/flapjack.xml @ 0:830715268b52 draft default tip
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author | cropgeeks |
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date | Tue, 14 Feb 2017 06:30:51 -0500 |
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-1:000000000000 | 0:830715268b52 |
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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> |