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comparison split-by-sample.xml @ 67:0a0a6be2d6b4 draft

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author cropgeeks
date Wed, 21 Feb 2018 11:57:13 -0500
parents d7e91a614582
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66:d709024d6bb4 67:0a0a6be2d6b4
1 <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">
2 <description>create a Flapjack project file from Flapjack formatted input files.</description>
3 <command><![CDATA[
4 python $__tool_directory__/FlapjackProject.py
5 -j $__tool_directory__/lib/flapjack.jar
6 -g $genotypes
7 -s $traits
8 #if $map
9 -m $map
10 #end if
11 #if $name
12 -n $name
13 #end if
14 #if $qtls
15 -q $qtls
16 #end if
17 #if $adv_opts.show_advanced
18 -M "$adv_opts.missingData"
19 -S "$adv_opts.hetSep"
20 #end if
21 ]]>
22 </command>
23 <inputs>
24 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
25 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
26
27 <param format="fjphenotype" name="traits" type="data" label="Flapjack phenotype file"
28 help="Flapjack-formatted (tab-delimited text) input file of phenotype data"/>
29
30 <param format="fjmap" name="map" type="data" label="Flapjack map file"
31 help="Flapjack-formatted (tab-delimited text) input file of map data"
32 optional="true"/>
33
34 <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
35 help="Flapjack-formatted (tab-delimited text) input file of QTL data"
36 optional="true"/>
37
38 <!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
39 <conditional name="adv_opts">
40 <param name="show_advanced" type="boolean"
41 label="Enable advanced options"
42 truevalue="show" falsevalue="">
43 </param>
44 <when value="show">
45 <param name="missingData" type="text" value="-"
46 label="Missing data string"
47 help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
48
49 <param name="hetSep" type="text" value="/"
50 label="Heterozygous allele separator string"
51 help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
52 </when>
53 </conditional>
54 <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
55 </inputs>
56
57 <outputs>
58 <data name="output" format="flapjack" />
59 </outputs>
60
61 <stdio>
62 <exit_code range="1:" />
63 </stdio>
64
65 <help><![CDATA[
66 .. class:: infomark
67
68 **What it does**
69
70 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
71 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
72
73 This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files.
74 See Flapjack's documentation_ for more details on the various Flapjack data formats.
75 More information on the CreateProject tool can be found here_
76
77 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
78 .. _here: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#createproject-exe-jhi-flapjack-io-createproject
79 ]]></help>
80
81 <citations>
82 <citation type="doi">10.1093/bioinformatics/btq580</citation>
83 </citations>
84 </tool>