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1 <tool id="Tassel" name="Tassel" version="2.0.0">
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2 <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
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3 <requirements>
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15
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4 <requirement type="package" version="5.2.89">tassel</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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8 <exit_code range="1:" level="fatal" />
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9 </stdio>
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17
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10 <command>
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11 #if $analysis_opts.fonction_selector == "ck":
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12 mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1;
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13 #else if $analysis_opts.fonction_selector == "ld":
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14 mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1;
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15 #else if $analysis_opts.fonction_selector == "glm":
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17
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16 #if $analysis_opts.add_file.additional_file_selector == "no":
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17 mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -combineA -input1 -input2 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2;
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18 #else if $analysis_opts.add_file.additional_file_selector == "yes":
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19 mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait -combineA -input1 -input2 -input3 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 -runfork3 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2;
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20 #end if
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17
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21 #else if $analysis_opts.fonction_selector == "mlm":
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22 #if $analysis_opts.add_structure_file.additional_file_selector == "no":
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23 mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork4 >>$log;mv tmpdir$$/output4.txt $output1;mv tmpdir$$/output5.txt $output2;mv tmpdir$$/output6.txt $output3;
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24 #else if $analysis_opts.add_structure_file.additional_file_selector == "yes":
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25 mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -input3 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork3 -runfork4 >>$log;mv tmpdir$$/output4.txt $output1;mv tmpdir$$/output5.txt $output2;mv tmpdir$$/output6.txt $output3;
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26 #end if
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27 #end if
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11
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28 </command>
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29 <inputs>
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30 <param format="txt" name="hapmap" type="data" label="HapMap file"/>
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31 <conditional name="analysis_opts">
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32 <param name="fonction_selector" type="select" label="Type of analysis">
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33 <option value="mlm" selected="True">MLM</option>
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34 <option value="glm">GLM</option>
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35 <option value="ld">Linkage Disequilibrium</option>
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36 <option value="ck">Kinship</option>
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37 </param>
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38 <when value="glm">
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39 <param format="txt" name="trait" type="data" label="Trait file"/>
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40 <conditional name="add_file">
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41 <param name="additional_file_selector" type="select" label="Add structure file">
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42 <option value="no" selected="True">no</option>
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43 <option value="yes">yes</option>
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44 </param>
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45 <when value="yes">
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46 <param format="txt" name="structure" type="data" label="Structure file"/>
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47 </when>
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48 <when value="no">
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49 </when>
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50 </conditional>
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51 </when>
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52 <when value="mlm">
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53 <param format="txt" name="trait" type="data" label="Trait file"/>
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54 <param format="txt" name="kinship" type="data" label="Kinship file"/>
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55 <conditional name="add_structure_file">
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56 <param name="additional_file_selector" type="select" label="Add structure file">
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57 <option value="no" selected="True">no</option>
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58 <option value="yes">yes</option>
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59 </param>
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60 <when value="yes">
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61 <param format="txt" name="structure" type="data" label="Structure file"/>
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62 </when>
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63 <when value="no">
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64 </when>
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65 </conditional>
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66 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
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67 <option value="P3D" selected="True">P3D</option>
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68 <option value="EachMarker">EachMarker</option>
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69 </param>
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70 <param name="mlmCompressionLevel" type="select" label="Compression Level">
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71 <option value="Optimum" selected="True">Optimum</option>
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72 <option value="Custom">Custom</option>
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73 <option value="None">None</option>
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74 </param>
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75 </when>
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76 <when value="ld"></when>
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77 <when value="ck"></when>
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78 </conditional>
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79 <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
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80 </inputs>
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81 <outputs>
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82 <data format="txt" name="output1" label="Tassel output">
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83 <change_format>
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84 <when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
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85 </change_format>
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86 </data>
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87
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88 <data format="txt" name="output2" label="Allele effects">
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89 <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
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90 </data>
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91
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92 <data format="txt" name="output3" label="Compression file">
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93 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
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94 </data>
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95
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96 <data format="txt" name="log" label="Log file"/>
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97 </outputs>
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98 <tests>
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99 <test>
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100 <param name="hapmap" value="input_hapmap.txt"/>
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101 <conditional name="analysis_opts">
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102 <param name="fonction_selector" value="glm"/>
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103 <param name="trait" value="phenotyping_DRB.csv"/>
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104 <conditional name="add_structure_file">
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105 <param name="additional_file_selector" value="yes"/>
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106 <param name="structure" value="Best_K_Output"/>
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107 </conditional>
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108 </conditional>
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109 <param name="filterAlignMinFreq" value="0.05"/>
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110 <output name="output1" value="Tassel_output.txt"/>
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111 <output name="output2" value="Allele_effects.txt"/>
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112 </test>
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113 </tests>
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114 <help><![CDATA[
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115 .. class:: infomark
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116
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117 **Tassel5** version 5.2.40
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118
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119 .. class:: infomark
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120
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121 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
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122
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123 .. class:: infomark
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124
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125 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
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126
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127 ---------------------------------------------------
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128
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129 =======
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130 Tassel5
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131 =======
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132
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133 -----------
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134 Description
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135 -----------
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136
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137 | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
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138 | For further informations on tassel, please visit the website_.
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139
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140 .. _website: http://www.maizegenetics.net/tassel/
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141
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142 ------------
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143 Dependencies
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144 ------------
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145
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146 Tassel5
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147
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148 tassel_ 5.2.40, Conda version
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149
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150 .. _tassel: https://anaconda.org/bioconda/tassel
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151
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9
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152 ]]></help>
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153 <citations>
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154 <citation type="doi">10.1093/bioinformatics/btm308</citation>
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155 </citations>
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156 </tool>
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