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