Mercurial > repos > cropgeeks > flapjack
comparison hapmap2fj.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_hapmap2fj" name="HapMap to Flapjack" version="0.0.1"> | |
| 2 | |
| 3 <!--System.out.println("Usage: hapmap2flapjack <options>\n" | |
| 4 + " where valid options are:\n" | |
| 5 + " -separator=<s or t> (required separator used in input file)\n" | |
| 6 + " -hapmap=<hapmap_file> (required input file)\n" | |
| 7 + " -map=<map_file> (required output file)\n" | |
| 8 + " -genotypes=<genotype_file> (required output file)\n");--> | |
| 9 | |
| 10 <description>convert an HapMap formatted file into a Flapjack-formatted genotype file</description> | |
| 11 <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.HapMapToFJTabbedConverter | |
| 12 -hapmap=$hapmap | |
| 13 -separator=$separator | |
| 14 -map=$map | |
| 15 -genotypes=$genotypes | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param format="txt" name="hapmap" type="data" label="Source file" | |
| 19 help="HapMap Formatted File"/> | |
| 20 <param name="separator" type="boolean" label="File is tab-separated" | |
| 21 truevalue="t" falsevalue="s"> | |
| 22 </param> | |
| 23 <param name="memory" type="select" label="Memory" | |
| 24 help="How much memory to use; larger files may require more memory"> | |
| 25 <option selected="true" value="64m">64MB</option> | |
| 26 <option value="128m">128MB</option> | |
| 27 <option value="256m">256MB</option> | |
| 28 </param> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data format="fjmap" name="map" /> | |
| 32 <data format="fjgenotype" name="genotypes" /> | |
| 33 </outputs> | |
| 34 | |
| 35 <stdio> | |
| 36 <exit_code range="1:" /> | |
| 37 </stdio> | |
| 38 | |
| 39 <help><![CDATA[ | |
| 40 .. class:: infomark | |
| 41 | |
| 42 **What it does** | |
| 43 | |
| 44 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, | |
| 45 allowing for rapid navigation and comparisons between lines, markers and chromosomes. | |
| 46 | |
| 47 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. | |
| 48 See Flapjack's documentation_ for more details on the various Flapjack data formats. | |
| 49 | |
| 50 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats | |
| 51 | |
| 52 | |
| 53 | |
| 54 ]]></help> | |
| 55 <citations> | |
| 56 <citation type="doi">10.1093/bioinformatics/btq580</citation> | |
| 57 </citations> | |
| 58 </tool> |