Mercurial > repos > cropgeeks > flapjack
comparison hdf52fj.xml @ 36:927533e85a6a draft
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| author | cropgeeks |
|---|---|
| date | Thu, 02 Mar 2017 06:14:46 -0500 |
| parents | |
| children | 8855844f40a8 |
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| 35:414aa590a1de | 36:927533e85a6a |
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| 1 <tool id="flapjack_hdf52fj" name="HDF5 to Flapjack" version="0.0.1"> | |
| 2 | |
| 3 <description>convert an HDF5 formatted genotype file into a Flapjack-formatted genotype file</description> | |
| 4 <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Hdf5ToFJTabbedConverter | |
| 5 -hdf5=$hdf5 | |
| 6 -lines=$lines | |
| 7 -markers=$markers | |
| 8 -missing_filter=$missing_filter | |
| 9 -heterozygous_filter=$heterozygous_filter | |
| 10 -genotypes=$genotypes | |
| 11 </command> | |
| 12 <inputs> | |
| 13 <param format="h5" name="hdf5" type="data" label="Source file" | |
| 14 help="Flapjack's flavour of HDF5 for storing genotype data."/> | |
| 15 <param format="txt" name="lines" type="data" label="Source file" | |
| 16 help="A list of lines desired in the output. One line name per line on each line of the file."/> | |
| 17 <param format="txt" name="markers" type="data" label="Source file" | |
| 18 help="A list of markers desired in the output. One line name per marker on each line of the file."/> | |
| 19 <param name="missing_filter" type="boolean" label="Filter out missing markers" | |
| 20 truevalue="true" falsevalue="false"> | |
| 21 </param> | |
| 22 <param name="heterozygous_filter" type="boolean" label="Filter out heterozygous markers" | |
| 23 truevalue="true" falsevalue="false"> | |
| 24 </param> | |
| 25 <param name="memory" type="select" label="Memory" | |
| 26 help="How much memory to use; larger files may require more memory"> | |
| 27 <option selected="true" value="64m">64MB</option> | |
| 28 <option value="128m">128MB</option> | |
| 29 <option value="256m">256MB</option> | |
| 30 </param> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="fjgenotype" name="genotypes" /> | |
| 34 </outputs> | |
| 35 | |
| 36 <help><![CDATA[ | |
| 37 .. class:: infomark | |
| 38 | |
| 39 **What it does** | |
| 40 | |
| 41 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, | |
| 42 allowing for rapid navigation and comparisons between lines, markers and chromosomes. | |
| 43 | |
| 44 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. | |
| 45 See Flapjack's documentation_ for more details on the various Flapjack data formats. | |
| 46 | |
| 47 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats | |
| 48 | |
| 49 | |
| 50 | |
| 51 ]]></help> | |
| 52 <citations> | |
| 53 <citation type="doi">10.1093/bioinformatics/btq580</citation> | |
| 54 </citations> | |
| 55 </tool> |