Mercurial > repos > cropgeeks > flapjack
comparison createproject.xml @ 4:8970bd921458 draft
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| author | cropgeeks |
|---|---|
| date | Tue, 21 Feb 2017 06:37:00 -0500 |
| parents | |
| children | 735f690bdb76 |
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| 3:0d040ceef479 | 4:8970bd921458 |
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| 1 <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1"> | |
| 2 | |
| 3 <!--System.out.println("Usage: createproject <options>\n" | |
| 4 + " where valid options are:\n" | |
| 5 + " -map=<map_file> (optional input file)\n" | |
| 6 + " -genotypes=<genotypes_file> (required input file)\n" | |
| 7 + " -traits=<traits_file> (optional input file)\n" | |
| 8 + " -qtls=<qtl_file> (optional input file)\n" | |
| 9 + " -decimalEnglish (optional input parameter)\n" | |
| 10 + " -project=<project_file> (required output file)\n");--> | |
| 11 | |
| 12 <description>Run pedigree verification of F1s (known parents) analysis</description> | |
| 13 <command><![CDATA[ | |
| 14 java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject | |
| 15 -map=$map -genotypes=$genotypes -galaxyHTML=$html -project=$output | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param format="fjmap" name="map" type="data" label="Flapjack map file" | |
| 20 help="Flapjack-formatted (tab-delimited text) input file of map data"/> | |
| 21 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" | |
| 22 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> | |
| 23 | |
| 24 <param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True" | |
| 25 label="Read input data using decimal English" | |
| 26 help="Build the index using a perfect hash rather than a dense hash. This will require less memory | |
| 27 (especially during quantification), but will take longer to construct "/> | |
| 28 <param name="memory" type="select" label="Memory" | |
| 29 help="How much memory to use; larger files may require more memory"> | |
| 30 <option selected="true" value="64m">64MB</option> | |
| 31 <option value="128m">128MB</option> | |
| 32 <option value="256m">256MB</option> | |
| 33 </param> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data name="output" format="flapjack" /> | |
| 37 <data name="html" format="html" /> | |
| 38 </outputs> | |
| 39 | |
| 40 <stdio> | |
| 41 <exit_code range="1:" /> | |
| 42 </stdio> | |
| 43 | |
| 44 <help><![CDATA[ | |
| 45 .. class:: infomark | |
| 46 | |
| 47 **What it does** | |
| 48 | |
| 49 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, | |
| 50 allowing for rapid navigation and comparisons between lines, markers and chromosomes. | |
| 51 | |
| 52 This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files. | |
| 53 See Flapjack's documentation_ for more details on the various Flapjack data formats. | |
| 54 | |
| 55 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats | |
| 56 | |
| 57 | |
| 58 | |
| 59 ]]></help> | |
| 60 <citations> | |
| 61 <citation type="doi">10.1093/bioinformatics/btq580</citation> | |
| 62 </citations> | |
| 63 </tool> |