|
4
|
1 <tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1">
|
|
|
2
|
|
|
3 <description>Run marker assisted backcrossing analysis on a dataset</description>
|
|
|
4
|
|
|
5 <command><![CDATA[
|
|
|
6 java
|
|
|
7 #if $advanced_options.show_advanced
|
|
|
8 -Xmx$advanced_options.memory
|
|
|
9 #end if
|
|
|
10 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
|
|
|
11 -map=$map
|
|
|
12 -genotypes=$genotypes
|
|
|
13 -qtls=$qtls
|
|
|
14 -parent1=$parent1
|
|
|
15 -parent2=$parent2
|
|
|
16 -model=$model
|
|
|
17 -coverage=$coverage
|
|
|
18 #if $advanced_options.show_advanced
|
|
|
19 $advanced_options.decimalEnglish
|
|
|
20 #end if
|
|
|
21 -output=$output
|
|
42
|
22 -project=$project
|
|
4
|
23 ]]></command>
|
|
|
24
|
|
|
25 <inputs>
|
|
|
26 <param format="fjmap" name="map" type="data" label="Flapjack map file"
|
|
|
27 help="Flapjack-formatted (tab-delimited text) input file of map data"/>
|
|
|
28 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
|
|
|
29 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
|
|
|
30 <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
|
|
|
31 help="Flapjack-formatted (tab-delimited text) input file of QTL data"/>
|
|
|
32 <param name="parent1" type="integer" value="1" label="Index of recurrent parent"
|
|
|
33 help="The index of the recurrent parent in the genotype file"/>
|
|
|
34 <param name="parent2" type="integer" value="2" label="Index of donor parent"
|
|
|
35 help="The index of the donor parent in the genotype file"/>
|
|
|
36 <param name="model" type="select" label="Model"
|
|
|
37 help="The model to use for calculating statistics">
|
|
|
38 <option selected="true" value="weighted">Weighted</option>
|
|
|
39 <option value="unweighted">Unweighted</option>
|
|
|
40 </param>
|
|
|
41 <param name="coverage" type="float" value="10" label="Maximum coverage of a marker"
|
|
|
42 help="The maximum length of genome a marker can represent"/>
|
|
|
43 <conditional name="advanced_options">
|
|
|
44 <param name="show_advanced" type="boolean" label="Enable advanced options"
|
|
|
45 truevalue="show" falsevalue="">
|
|
|
46 </param>
|
|
|
47 <when value="show">
|
|
|
48 <param name="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
|
|
|
49 label="Force English-style decimal marks"
|
|
|
50 help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy's locale settings"/>
|
|
|
51 <param name="memory" type="select" label="Memory"
|
|
|
52 help="How much memory to use; larger files may require more memory">
|
|
|
53 <option selected="true" value="64m">64MB</option>
|
|
|
54 <option value="128m">128MB</option>
|
|
|
55 <option value="256m">256MB</option>
|
|
|
56 </param>
|
|
|
57 </when>
|
|
|
58 </conditional>
|
|
|
59 </inputs>
|
|
|
60
|
|
|
61 <outputs>
|
|
|
62 <data format="tabular" name="output" />
|
|
42
|
63 <data format="flapjack" name="project" />
|
|
4
|
64 </outputs>
|
|
|
65
|
|
|
66 <stdio>
|
|
|
67 <exit_code range="1:" />
|
|
|
68 </stdio>
|
|
|
69
|
|
|
70 <help><![CDATA[
|
|
|
71 .. class:: infomark
|
|
|
72
|
|
|
73 **What it does**
|
|
|
74
|
|
|
75 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
|
|
|
76 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
|
|
|
77
|
|
|
78 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
|
|
|
79 See Flapjack's documentation_ for more details on the various Flapjack data formats.
|
|
|
80
|
|
|
81 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
|
|
|
82
|
|
|
83 ]]></help>
|
|
|
84 <citations>
|
|
|
85 <citation type="doi">10.1093/bioinformatics/btq580</citation>
|
|
|
86 </citations>
|
|
|
87 </tool> |
