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comparison mabcstats.xml @ 54:8855844f40a8 draft

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Uploaded the latest version of our Flapjack tools for Galaxy.
author cropgeeks
date Tue, 14 Nov 2017 06:42:48 -0500
parents 3e426561ac83
children 6777844fd638
comparison
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53:1de63acd6b12 54:8855844f40a8
1 <tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1"> 1 <tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1">
2 <description>Run marker assisted backcrossing (MABC) analysis on a dataset</description>
3 <command><![CDATA[
4 java
5 #if $adv_opts.show_advanced
6 -Xmx$adv_opts.memory
7 #end if
8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
9 -m $map
10 -g $genotypes
11 -q $qtls
12 -r $parent1
13 -d $parent2
14 -model $model
15 -c $coverage
16 -o $output
17 #if $adv_opts.show_advanced
18 $adv_opts.allChromosomes
19 $adv_opts.collapseHets
20 -M "$adv_opts.missingData"
21 -S "$adv_opts.hetSep"
22 $adv_opts.transposed
23 $adv_opts.decimalEnglish
24 #end if
25 #if $create_project
26 -p $project
27 #end if
28 ]]></command>
2 29
3 <description>Run marker assisted backcrossing analysis on a dataset</description> 30 <inputs>
31 <param format="fjmap" name="map" type="data"
32 label="Flapjack map file"
33 help="Flapjack-formatted (tab-delimited text) input file of map data."/>
4 34
5 <command><![CDATA[ 35 <param format="fjgenotype" name="genotypes" type="data"
6 java 36 label="Flapjack genotype file"
7 #if $advanced_options.show_advanced 37 help="Flapjack-formatted (tab-delimited text) input file of genotype data."/>
8 -Xmx$advanced_options.memory
9 #end if
10 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
11 -m $map
12 -g $genotypes
13 -q $qtls
14 -r $parent1
15 -d $parent2
16 -model $model
17 -c $coverage
18 #if $advanced_options.show_advanced
19 $advanced_options.decimalEnglish
20 #end if
21 -o $output
22 #if $create_project
23 -p $project
24 #end if
25 ]]></command>
26 38
27 <inputs> 39 <param format="fjqtl" name="qtls" type="data"
28 <param format="fjmap" name="map" type="data" label="Flapjack map file" 40 label="Flapjack QTL file"
29 help="Flapjack-formatted (tab-delimited text) input file of map data"/> 41 help="Flapjack-formatted (tab-delimited text) input file of QTL data."/>
30 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" 42
31 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> 43 <param name="parent1" type="integer" value="1"
32 <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file" 44 label="Index of recurrent parent"
33 help="Flapjack-formatted (tab-delimited text) input file of QTL data"/> 45 help="The index of the recurrent parent in the genotype file."/>
34 <param name="parent1" type="integer" value="1" label="Index of recurrent parent" 46
35 help="The index of the recurrent parent in the genotype file"/> 47 <param name="parent2" type="integer" value="2"
36 <param name="parent2" type="integer" value="2" label="Index of donor parent" 48 label="Index of donor parent"
37 help="The index of the donor parent in the genotype file"/> 49 help="The index of the donor parent in the genotype file."/>
38 <param name="model" type="select" label="Model" 50
39 help="The model to use for calculating statistics"> 51 <param name="model" type="select"
40 <option selected="true" value="weighted">Weighted</option> 52 label="Model"
41 <option value="unweighted">Unweighted</option> 53 help="The model to use for calculating statistics.">
42 </param> 54 <option selected="true" value="weighted">Weighted</option>
43 <param name="coverage" type="float" value="10" label="Maximum coverage of a marker" 55 <option value="unweighted">Unweighted</option>
44 help="The maximum length of genome a marker can represent"/>
45 <conditional name="advanced_options">
46 <param name="show_advanced" type="boolean" label="Enable advanced options"
47 truevalue="show" falsevalue="">
48 </param> 56 </param>
49 <when value="show"> 57
50 <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="True" 58 <param name="coverage" type="float" value="10" label="Maximum coverage of a marker"
51 label="Force English-style decimal marks" 59 help="The maximum length of genome a marker can represent."/>
52 help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy's locale settings"/> 60
53 <param name="memory" type="select" label="Memory" 61 <conditional name="adv_opts">
54 help="How much memory to use; larger files may require more memory"> 62 <param name="show_advanced" type="boolean"
55 <option selected="true" value="64m">64MB</option> 63 label="Enable advanced options"
56 <option value="128m">128MB</option> 64 truevalue="show" falsevalue="">
57 <option value="256m">256MB</option>
58 </param> 65 </param>
59 </when> 66 <when value="show">
60 </conditional> 67 <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
61 68 label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
62 <param name="create_project" type="boolean" label="Also create Flapjack project file" 69 help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>
63 truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results."> 70
64 </param> 71 <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
65 </inputs> 72 label="Don't distinguish between heterozygous alleles"
73 help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
74
75 <param name="missingData" type="text" value="-"
76 label="Missing data string"
77 help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
78
79 <param name="hetSep" type="text" value="/"
80 label="Heterozygous allele separator string"
81 help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
82
83 <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
84 label="Genotype data has been transposed"
85 help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
86
87 <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
88 label="Force English-style decimal marks"
89 help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/>
90
91 <param name="memory" type="select"
92 label="Memory"
93 help="How much memory to use (larger files may require more memory).">
94 <option selected="true" value="64m">64MB</option>
95 <option value="128m">128MB</option>
96 <option value="256m">256MB</option>
97 </param>
98 </when>
99 </conditional>
100
101 <param name="create_project" type="boolean" label="Also create Flapjack project file"
102 truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results.">
103 </param>
104 </inputs>
66 105
67 <outputs> 106 <outputs>
68 <data format="tabular" name="output" /> 107 <data format="tabular" name="output" />
69 <data format="flapjack" name="project"> 108 <data format="flapjack" name="project">
70 <filter>create_project</filter> 109 <filter>create_project</filter>
71 </data> 110 </data>
72 111 </outputs>
73 </outputs>
74 112
75 <stdio> 113 <stdio>
76 <exit_code range="1:" /> 114 <exit_code range="1:" />
77 </stdio> 115 </stdio>
78 116
79 <help><![CDATA[ 117 <help><![CDATA[
80 .. class:: infomark 118 .. class:: infomark
81 119
82 **What it does** 120 **What it does**
83 121
84 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, 122 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
85 allowing for rapid navigation and comparisons between lines, markers and chromosomes. 123 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
86 124
87 This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. 125 Flapjack documentation_
88 See Flapjack's documentation_ for more details on the various Flapjack data formats.
89 126
90 .. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 127 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#mabcstats-exe-jhi-flapjack-io-generatemabcstats
128 ]]></help>
91 129
92 ]]></help> 130 <citations>
93 <citations> 131 <citation type="doi">10.1093/bioinformatics/btq580</citation>
94 <citation type="doi">10.1093/bioinformatics/btq580</citation> 132 </citations>
95 </citations>
96 </tool> 133 </tool>