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comparison pedverf1stats.xml @ 4:8970bd921458 draft

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author cropgeeks
date Tue, 21 Feb 2017 06:37:00 -0500
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3:0d040ceef479 4:8970bd921458
1 <tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1">
2
3 <!--System.out.println("Usage: pedverf1sstats <options>\n"
4 + " where valid options are:\n"
5 + " -map=<map_file> (required input file)\n"
6 + " -genotypes=<genotypes_file> (required input file)\n"
7 + " -parent1=<index_of_line> (required parameter, first line is index 1)\n"
8 + " -parent2=<index_of_line> (required parameter, first line is index 1)\n"
9 + " -expectedf1=<index_of_line> (optional parameter, first line is index 1)\n"
10 + " -decimalEnglish (optional parameter)\n"
11 + " -output=<output_file> (required output file)\n");-->
12
13 <description>Run pedigree verification of F1s (known parents) analysis</description>
14 <command><![CDATA[
15 java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats
16 -map=$map -genotypes=$genotypes -parent1=$parent1 -parent2=$parent2
17 #if $simulate_f1.simulate_f1_selector == "file":
18 -expectedf1=$simulate_f1.expectedF1
19 #end if
20 $decimalEnglish -output=$output
21 ]]>
22 </command>
23 <inputs>
24 <param format="csv,tabular,txt" name="map" type="data" label="Flapjack map file"
25 help="Flapjack-formatted (tab-delimited text) input file of map data"/>
26 <param format="csv,tabular,txt" name="genotypes" type="data" label="Flapjack genotype file"
27 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
28 <param name="parent1" type="integer" value="1" label="Index of parent 1"
29 help="The index of the first parent in the genotype file"/>
30 <param name="parent2" type="integer" value="2" label="Index of parent 2"
31 help="The index of the second parent in the genotype file"/>
32
33 <conditional name="simulate_f1">
34 <param name="simulate_f1_selector" type="select" label="Simulate expected F1 (or use F1 from file)">
35 <option value="simulate" selected="True">Simulate</option>
36 <option value="file">Select from file</option>
37 </param>
38 <when value="file">
39 <param argument="-expectedF1" type="integer" value="3" label="Index of expected F1"
40 help="The index of the donor parent in the genotype file"/>
41 </when>
42 </conditional>
43
44 <param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
45 label="Read input data using decimal English"
46 help="Build the index using a perfect hash rather than a dense hash. This will require less memory
47 (especially during quantification), but will take longer to construct "/>
48 <param name="memory" type="select" label="Memory"
49 help="How much memory to use; larger files may require more memory">
50 <option selected="true" value="64m">64MB</option>
51 <option value="128m">128MB</option>
52 <option value="256m">256MB</option>
53 </param>
54 </inputs>
55 <outputs>
56 <data format="tabular" name="output" />
57 </outputs>
58
59 <stdio>
60 <exit_code range="1:" />
61 </stdio>
62
63 <help><![CDATA[
64 .. class:: infomark
65
66 **What it does**
67
68 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
69 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
70
71 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
72 See Flapjack's documentation_ for more details on the various Flapjack data formats.
73
74 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
75
76
77
78 ]]></help>
79 <citations>
80 <citation type="doi">10.1093/bioinformatics/btq580</citation>
81 </citations>
82 </tool>