Mercurial > repos > cropgeeks > flapjack
view pedverf1stats.xml @ 41:8c12e46f652d draft
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author | cropgeeks |
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date | Thu, 02 Mar 2017 08:43:30 -0500 |
parents | 8970bd921458 |
children | 8855844f40a8 |
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<tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1"> <!--System.out.println("Usage: pedverf1sstats <options>\n" + " where valid options are:\n" + " -map=<map_file> (required input file)\n" + " -genotypes=<genotypes_file> (required input file)\n" + " -parent1=<index_of_line> (required parameter, first line is index 1)\n" + " -parent2=<index_of_line> (required parameter, first line is index 1)\n" + " -expectedf1=<index_of_line> (optional parameter, first line is index 1)\n" + " -decimalEnglish (optional parameter)\n" + " -output=<output_file> (required output file)\n");--> <description>Run pedigree verification of F1s (known parents) analysis</description> <command><![CDATA[ java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats -map=$map -genotypes=$genotypes -parent1=$parent1 -parent2=$parent2 #if $simulate_f1.simulate_f1_selector == "file": -expectedf1=$simulate_f1.expectedF1 #end if $decimalEnglish -output=$output ]]> </command> <inputs> <param format="fjmap" name="map" type="data" label="Flapjack map file" help="Flapjack-formatted (tab-delimited text) input file of map data"/> <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> <param name="parent1" type="integer" value="1" label="Index of parent 1" help="The index of the first parent in the genotype file"/> <param name="parent2" type="integer" value="2" label="Index of parent 2" help="The index of the second parent in the genotype file"/> <conditional name="simulate_f1"> <param name="simulate_f1_selector" type="select" label="Simulate expected F1 (or use F1 from file)"> <option value="simulate" selected="True">Simulate</option> <option value="file">Select from file</option> </param> <when value="file"> <param argument="-expectedF1" type="integer" value="3" label="Index of expected F1" help="The index of the donor parent in the genotype file"/> </when> </conditional> <param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True" label="Read input data using decimal English" help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification), but will take longer to construct "/> <param name="memory" type="select" label="Memory" help="How much memory to use; larger files may require more memory"> <option selected="true" value="64m">64MB</option> <option value="128m">128MB</option> <option value="256m">256MB</option> </param> </inputs> <outputs> <data format="tabular" name="output" /> </outputs> <stdio> <exit_code range="1:" /> </stdio> <help><![CDATA[ .. class:: infomark **What it does** Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, allowing for rapid navigation and comparisons between lines, markers and chromosomes. This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. See Flapjack's documentation_ for more details on the various Flapjack data formats. .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btq580</citation> </citations> </tool>