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1 <tool id="Tassel" name="Tassel" version="5.0">
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2 <description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description>
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3 <requirements>
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4 <requirement type="package" version="5.0">tassel</requirement>
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5 </requirements>
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6 <command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
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7 #if $analysis_opts.fonction_selector == "mlm":
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8 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
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9 -fork2 -r $analysis_opts.trait
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10 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
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11 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
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12 #end if
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13 -fork4 -k $analysis_opts.kinship
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14 -combineA -input1 -input2
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15 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
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16 -input3
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17 #end if
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18 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2
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19 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
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20 -runfork3
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21 #end if
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22 -runfork4
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23
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24 #else if $analysis_opts.fonction_selector == "glm":
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25 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
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26 -fork2 -r $analysis_opts.trait
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27 #if $analysis_opts.add_file.additional_file_selector == "yes":
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28 -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
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29 #end if
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30 -combineA -input1 -input2
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31 #if $analysis_opts.add_file.additional_file_selector == "yes":
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32 -input3
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33 #end if
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34 -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
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35 #if $analysis_opts.add_file.additional_file_selector == "yes":
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36 -runfork3
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37 #end if
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38 #else if $analysis_opts.fonction_selector == "ld":
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39 -fork1 -h $hapmap
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40 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
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41 #else if $analysis_opts.fonction_selector == "ck":
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42 -fork1 -h $hapmap
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43 -ck -export tmpdir$$/kinship -runfork1
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44 #end if
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45 </command>
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46 <inputs>
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47 <param format="txt" name="hapmap" type="data" label="HapMap file"/>
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48 <conditional name="analysis_opts">
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49 <param name="fonction_selector" type="select" label="Type of analysis">
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50 <option value="mlm" selected="True">MLM</option>
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51 <option value="glm">GLM</option>
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52 <option value="ld">Linkage Disequilibrium</option>
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53 <option value="ck">Kinship</option>
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54 </param>
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55 <when value="glm">
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56 <param format="txt" name="trait" type="data" label="Trait file"/>
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57 <conditional name="add_file">
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58 <param name="additional_file_selector" type="select" label="Add structure file">
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59 <option value="no" selected="True">no</option>
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60 <option value="yes">yes</option>
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61 </param>
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62 <when value="yes">
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63 <param format="txt" name="structure" type="data" label="Structure file"/>
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64 </when>
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65 </conditional>
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66 </when>
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67 <when value="mlm">
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68 <param format="txt" name="trait" type="data" label="Trait file"/>
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69 <param format="txt" name="kinship" type="data" label="Kinship file"/>
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70 <conditional name="add_structure_file">
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71 <param name="additional_file_selector" type="select" label="Add structure file">
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72 <option value="no" selected="True">no</option>
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73 <option value="yes">yes</option>
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74 </param>
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75 <when value="yes">
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76 <param format="txt" name="structure" type="data" label="Structure file"/>
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77 </when>
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78 </conditional>
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79 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
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80 <option value="P3D" selected="True">P3D</option>
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81 <option value="EachMarker">EachMarker</option>
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82 </param>
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83 <param name="mlmCompressionLevel" type="select" label="Compression Level">
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84 <option value="Optimum" selected="True">Optimum</option>
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85 <option value="Custom">Custom</option>
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86 <option value="None">None</option>
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87 </param>
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88 </when>
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89 <when value="ld"></when>
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90 <when value="ck"></when>
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91 </conditional>
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92 <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
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93 </inputs>
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94 <outputs>
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95 <data format="txt" name="output1" label="Tassel output">
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96 <change_format>
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97 <when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
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98 </change_format>
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99 </data>
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100
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101 <data format="txt" name="output2" label="Allele effects">
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102 <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
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103 </data>
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104
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105 <data format="txt" name="output3" label="Compression file">
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106 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
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107 </data>
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108
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109 <data format="txt" name="log" label="Log file"/>
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110 </outputs>
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111 <help>
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112
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113 .. class:: infomark
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114
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115 **Program encapsulated in Galaxy by Southgreen**
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116
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117 .. class:: infomark
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118
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119 **Tassel**
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120
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121 -----
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122
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123 ==========
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124 Authors:
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125 ==========
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126
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127 **Terry Casstevens**
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128
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129 -----
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130
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131 ==========
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132 Overview
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133 ==========
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134
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135 Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
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136
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137 -----
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138
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139 For further informations, please visite the website of TASSEL_.
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140
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141
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142 .. _TASSEL: http://www.maizegenetics.net/tassel/
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143
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144 </help>
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145 <!--
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146 <tests>
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147 <test>
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148 <param name="input" value="genotyping_file.inp" />
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149 <output name="output" file="phase_output" />
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150 </test>
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151 </tests>
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152 -->
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153 </tool>
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