Mercurial > repos > cropgeeks > flapjack

annotate mabcstats.xml @ 58:ca8171e44b7e draft

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author cropgeeks
date Fri, 17 Nov 2017 06:20:15 -0500
parents 8a06f49972d0
children 3ff3493f54d6
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1 <tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1">
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2 <description>run marker assisted backcrossing (MABC) analysis on a dataset</description>
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3 <command><![CDATA[
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4 java
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5 #if $adv_opts.show_advanced
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6 -Xmx$adv_opts.memory
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7 #end if
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8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
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9 -m $map
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10 -g $genotypes
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11 -q $qtls
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12 #if $traits
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13 -t $traits
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14 #end if
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15 -r $parent1
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16 -d $parent2
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17 -model $model
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18 -c $coverage
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19 -o $output
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20 #if $adv_opts.show_advanced
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21 $adv_opts.allChromosomes
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22 $adv_opts.collapseHets
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23 -M "$adv_opts.missingData"
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24 -S "$adv_opts.hetSep"
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25 $adv_opts.transposed
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26 $adv_opts.decimalEnglish
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27 #end if
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28 #if $create_project
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29 -p $project
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30 #end if
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31 ]]></command>
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32
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33 <inputs>
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34 <param format="fjmap" name="map" type="data"
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35 label="Flapjack map file"
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36 help="Flapjack-formatted (tab-delimited text) input file of map data."/>
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37
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38 <param format="fjgenotype" name="genotypes" type="data"
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39 label="Flapjack genotype file"
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40 help="Flapjack-formatted (tab-delimited text) input file of genotype data."/>
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41
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42 <param format="fjqtl" name="qtls" type="data"
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43 label="Flapjack QTL file"
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44 help="Flapjack-formatted (tab-delimited text) input file of QTL data."/>
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45
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46 <param format="fjphenotype" name="traits" type="data"
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47 label="Flapjack Trait file"
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48 help="Flapjack-formatted (tab-delimited text) input file of trait data."
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49 optional="true"/>
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50
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51 <param name="parent1" type="integer" value="1"
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52 label="Index of recurrent parent"
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53 help="The index of the recurrent parent in the genotype file."/>
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54
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55 <param name="parent2" type="integer" value="2"
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56 label="Index of donor parent"
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57 help="The index of the donor parent in the genotype file."/>
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58
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59 <param name="model" type="select"
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60 label="Model"
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61 help="The model to use for calculating statistics.">
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62 <option selected="true" value="weighted">Weighted</option>
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63 <option value="unweighted">Unweighted</option>
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64 </param>
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65
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66 <param name="coverage" type="float" value="10" label="Maximum coverage of a marker"
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67 help="The maximum length of genome a marker can represent."/>
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68
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69 <param name="exclude_parents" type="boolean" label="Exclude parental lines which have not been selected."
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70 truevalue="true" falsevalue="false" help="Excludes parental lines which have not been selected as the recurrent, or donor parent from the analysis and results.">
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71 </param>
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72
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73 <conditional name="adv_opts">
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74 <param name="show_advanced" type="boolean"
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75 label="Enable advanced options"
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76 truevalue="show" falsevalue="">
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77 </param>
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78 <when value="show">
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79 <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
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80 label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
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81 help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>
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82
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83 <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
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84 label="Don't distinguish between heterozygous alleles"
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85 help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
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86
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87 <param name="missingData" type="text" value="-"
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88 label="Missing data string"
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89 help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
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90
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91 <param name="hetSep" type="text" value="/"
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92 label="Heterozygous allele separator string"
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93 help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
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94
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95 <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
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96 label="Genotype data has been transposed"
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97 help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
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98
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99 <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
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100 label="Force English-style decimal marks"
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101 help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/>
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102
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103 <param name="memory" type="select"
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104 label="Memory"
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105 help="How much memory to use (larger files may require more memory).">
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106 <option selected="true" value="64m">64MB</option>
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107 <option value="128m">128MB</option>
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108 <option value="256m">256MB</option>
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109 </param>
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110 </when>
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111 </conditional>
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112
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113 <param name="create_project" type="boolean" label="Also create Flapjack project file"
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114 truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results.">
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115 </param>
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116 </inputs>
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117
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118 <outputs>
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119 <data format="tabular" name="output" />
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120 <data format="flapjack" name="project">
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121 <filter>create_project</filter>
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122 </data>
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123 </outputs>
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124
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125 <stdio>
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126 <exit_code range="1:" />
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127 </stdio>
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128
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129 <help><![CDATA[
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130 .. class:: infomark
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131
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132 **What it does**
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133
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134 Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
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135 allowing for rapid navigation and comparisons between lines, markers and chromosomes.
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136
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137 Flapjack documentation_
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138
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139 .. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#mabcstats-exe-jhi-flapjack-io-generatemabcstats
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140 ]]></help>
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141
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142 <citations>
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143 <citation type="doi">10.1093/bioinformatics/btq580</citation>
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144 </citations>
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145 </tool>