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1 <tool id="beta_diversity" name="beta_diversity" version="2.0.0">
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2 <description>Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables</description>
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3 <requirements>
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4 <requirement type="binary">beta_diversity.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 --galaxy_outputdir=$__new_file_path__
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9 #set datasets = []
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10 #set $path = ""
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11 #if $binary_chisq.__str__ != "None":
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12 #set datasets = $datasets + ["'binary_chisq_.*$:'" + $binary_chisq.__str__]
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13 #if path == "":
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14 #set $path=$binary_chisq.extra_files_path
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15 #end if
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16 #end if
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17 #if $binary_chord.__str__ != "None":
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18 #set datasets = $datasets + ["'binary_chord_.*$:'" + $binary_chord.__str__]
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19 #if path == "":
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20 #set $path=$binary_chord.extra_files_path
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21 #end if
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22 #end if
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23 #if $binary_euclidean.__str__ != "None":
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24 #set datasets = $datasets + ["'binary_euclidean_.*$:'" + $binary_euclidean.__str__]
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25 #if path == "":
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26 #set $path=$binary_euclidean.extra_files_path
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27 #end if
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28 #end if
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29 #if $binary_hamming.__str__ != "None":
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30 #set datasets = $datasets + ["'binary_hamming_.*$:'" + $binary_hamming.__str__]
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31 #if path == "":
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32 #set $path=$binary_hamming.extra_files_path
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33 #end if
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34 #end if
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35 #if $binary_jaccard.__str__ != "None":
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36 #set datasets = $datasets + ["'binary_jaccard_.*$:'" + $binary_jaccard.__str__]
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37 #if path == "":
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38 #set $path=$binary_jaccard.extra_files_path
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39 #end if
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40 #end if
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41 #if $binary_lennon.__str__ != "None":
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42 #set datasets = $datasets + ["'binary_lennon_.*$:'" + $binary_lennon.__str__]
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43 #if path == "":
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44 #set $path=$binary_lennon.extra_files_path
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45 #end if
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46 #end if
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47 #if $binary_ochiai.__str__ != "None":
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48 #set datasets = $datasets + ["'binary_ochiai_.*$:'" + $binary_ochiai.__str__]
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49 #if path == "":
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50 #set $path=$binary_ochiai.extra_files_path
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51 #end if
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52 #end if
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53 #if $binary_pearson.__str__ != "None":
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54 #set datasets = $datasets + ["'binary_pearson_.*$:'" + $binary_pearson.__str__]
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55 #if path == "":
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56 #set $path=$binary_pearson.extra_files_path
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57 #end if
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58 #end if
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59 #if $binary_sorensen_dice.__str__ != "None":
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60 #set datasets = $datasets + ["'binary_sorensen_dice_.*$:'" + $binary_sorensen_dice.__str__]
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61 #if path == "":
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62 #set $path=$binary_sorensen.extra_files_path
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63 #end if
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64 #end if
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65 #if $bray_curtis.__str__ != "None":
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66 #set datasets = $datasets + ["'bray_curtis_.*$:'" + $bray_curtis.__str__]
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67 #if path == "":
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68 #set $path=$bray_curtis.extra_files_path
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69 #end if
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70 #end if
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71 #if $canberra.__str__ != "None":
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72 #set datasets = $datasets + ["'canberra_.*$:'" + $canberra.__str__]
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73 #if path == "":
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74 #set $path=$canberra.extra_files_path
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75 #end if
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76 #end if
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77 #if $chisq.__str__ != "None":
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78 #set datasets = $datasets + ["'chisq_.*$:'" + $chisq.__str__]
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79 #if path == "":
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80 #set $path=$binary_euclidean.extra_files_path
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81 #end if
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82 #end if
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83 #if $chord.__str__ != "None":
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84 #set datasets = $datasets + ["'chord_.*$:'" + $chord.__str__]
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85 #if path == "":
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86 #set $path=$chord.extra_files_path
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87 #end if
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88 #end if
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89 #if $euclidean.__str__ != "None":
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90 #set datasets = $datasets + ["'euclidean_.*$:'" + $euclidean.__str__]
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91 #if path == "":
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92 #set $path=$euclidean.extra_files_path
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93 #end if
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94 #end if
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95 #if $gower.__str__ != "None":
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96 #set datasets = $datasets + ["'gower_.*$:'" + $gower.__str__]
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97 #if path == "":
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98 #set $path=$gower.extra_files_path
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99 #end if
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100 #end if
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101 #if $hellinger.__str__ != "None":
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102 #set datasets = $datasets + ["'hellinger_.*$:'" + $hellinger.__str__]
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103 #if path == "":
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104 #set $path=$hellinger.extra_files_path
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105 #end if
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106 #end if
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107 #if $kulczynski.__str__ != "None":
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108 #set datasets = $datasets + ["'kulczynski_.*$:'" + $kulczynski.__str__]
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109 #if path == "":
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110 #set $path=$kulczynski.extra_files_path
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111 #end if
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112 #end if
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113 #if $manhattan.__str__ != "None":
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114 #set datasets = $datasets + ["'manhattan_.*$:'" + $manhattan.__str__]
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115 #if path == "":
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116 #set $path=$manhattan.extra_files_path
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117 #end if
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118 #end if
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119 #if $morisita_horn.__str__ != "None":
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120 #set datasets = $datasets + ["'morisita_horn_.*$:'" + $morisita_horn.__str__]
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121 #if path == "":
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122 #set $path=$morisita_horn.extra_files_path
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123 #end if
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124 #end if
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125 #if $pearson.__str__ != "None":
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126 #set datasets = $datasets + ["'pearson_.*$:'" + $pearson.__str__]
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127 #if path == "":
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128 #set $path=$pearson.extra_files_path
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129 #end if
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130 #end if
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131 #if $soergel.__str__ != "None":
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132 #set datasets = $datasets + ["'soergel_.*$:'" + $soergel.__str__]
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133 #if path == "":
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134 #set $path=$soergel.extra_files_path
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135 #end if
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136 #end if
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137 #if $spearman_approx.__str__ != "None":
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138 #set datasets = $datasets + ["'spearman_approx_.*$:'" + $spearman_approx.__str__]
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139 #if path == "":
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140 #set $path=$spearman_approx.extra_files_path
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141 #end if
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142 #end if
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143 #if $specprof.__str__ != "None":
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144 #set datasets = $datasets + ["'specprof_.*$:'" + $specprof.__str__]
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145 #if path == "":
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146 #set $path=$specprof.extra_files_path
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147 #end if
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148 #end if
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149 #if $unifrac.__str__ != "None":
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150 #set datasets = $datasets + ["'unifrac_.*$:'" + $unifrac.__str__]
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151 #if path == "":
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152 #set $path=$unifrac.extra_files_path
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153 #end if
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154 #end if
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155 #if $unifrac_g.__str__ != "None":
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156 #set datasets = $datasets + ["'unifrac_g_.*$:'" + $unifrac_g.__str__]
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157 #if path == "":
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158 #set $path=$unifrac_g.extra_files_path
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159 #end if
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160 #end if
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161 #if $unifrac_g_full_tree.__str__ != "None":
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162 #set datasets = $datasets + ["'unifrac_g_full_tree_.*$:'" + $unifrac_g_full_tree.__str__]
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163 #if path == "":
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164 #set $path=$unifrac_g_full_tree.extra_files_path
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165 #end if
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166 #end if
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167 #if $unweighted_unifrac.__str__ != "None":
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168 #set datasets = $datasets + ["'unweighted_unifrac_.*$:'" + $unweighted_unifrac.__str__]
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169 #if path == "":
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170 #set $path=$unweighted_unifrac.extra_files_path
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171 #end if
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172 #end if
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173 #if $unweighted_unifrac_full_tree.__str__ != "None":
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174 #set datasets = $datasets + ["'unweighted_unifrac_full_tree_.*$:'" + $unweighted_unifrac_full_tree.__str__]
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175 #if path == "":
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176 #set $path=$unweighted_unifrac_full_tree.extra_files_path
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177 #end if
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178 #end if
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179 #if $weighted_normalized_unifrac.__str__ != "None":
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180 #set datasets = $datasets + ["'weighted_normalized_unifrac_.*$:'" + $weighted_normalized_unifrac.__str__]
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181 #if path == "":
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182 #set $path=$weighted_normalized_unifrac.extra_files_path
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183 #end if
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184 #end if
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185 #if $weighted_unifrac.__str__ != "None":
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186 #set datasets = $datasets + ["'weighted_unifrac_.*$:'" + $weighted_unifrac.__str__]
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187 #if path == "":
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188 #set $path=$weighted_unifrac.extra_files_path
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189 #end if
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190 #end if
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191 --galaxy_datasets=#echo ','.join($datasets)
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192 --galaxy_new_files_path='$path'
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193 beta_diversity.py
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194 --input_path=$input_path
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195 #if $rows.__str__ != '':
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196 --rows=$rows
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197 #end if
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198 --output_dir=$__new_file_path__
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199 --metrics=$metrics
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200 #if $tree_path.__str__ != "None" and len($tree_path.__str__) > 0:
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201 --tree_path=$tree_path
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202 #end if
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203 $full_tree
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204 </command>
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205 <inputs>
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206 <param name="input_path" type="data" format="qiimeotutable" label="input_path"
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207 help="input path: otu table (e.g., output from make_otu_table or single_rarefaction)"/>
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208 <param name="rows" type="text" label="rows"
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209 help="compute only these rows of the distance matrix. pass a list of sample names, e.g. 's1,s3' [by default, + the full n x n matrix is generated]"/>
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210 <param name="metrics" type="select" multiple="true" label="metrics" help="metrics to use">
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211 <option value="abund_jaccard">abund_jaccard</option>
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212 <option value="binary_chisq">binary_chisq</option>
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213 <option value="binary_chord">binary_chord</option>
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214 <option value="binary_euclidean">binary_euclidean</option>
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215 <option value="binary_hamming">binary_hamming</option>
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216 <option value="binary_jaccard">binary_jaccard</option>
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217 <option value="binary_lennon">binary_lennon</option>
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218 <option value="binary_ochiai">binary_ochiai</option>
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219 <option value="binary_otu_gain">binary_otu_gain</option>
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220 <option value="binary_pearson">binary_pearson</option>
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221 <option value="binary_sorensen_dice">binary_sorensen_dice</option>
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222 <option value="bray_curtis">bray_curtis</option>
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223 <option value="canberra">canberra</option>
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224 <option value="chisq">chisq</option>
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225 <option value="chord">chord</option>
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226 <option value="euclidean">euclidean</option>
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227 <option value="gower">gower</option>
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228 <option value="hellinger">hellinger</option>
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229 <option value="kulczynski">kulczynski</option>
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230 <option value="manhattan">manhattan</option>
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231 <option value="morisita_horn">morisita_horn</option>
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232 <option value="pearson">pearson</option>
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233 <option value="soergel">soergel</option>
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234 <option value="spearman_approx">spearman_approx</option>
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235 <option value="specprof">specprof</option>
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236 <option value="unifrac">unifrac</option>
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237 <option value="unifrac_g">unifrac_g</option>
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238 <option value="unifrac_g_full_tree">unifrac_g_full_tree</option>
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239 <option value="unweighted_unifrac">unweighted_unifrac</option>
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240 <option value="unweighted_unifrac_full_tree">unweighted_unifrac_full_tree</option>
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241 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
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242 <option value="weighted_unifrac">weighted_unifrac</option>
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243 </param>
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244 <param name="tree_path" type="data" optional="true" label="tree_path"
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245 help="path to newick tree file, required for phylogenetic metrics [default: None]"/>
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246 <param name="full_tree" type="boolean" truevalue="--full_tree" falsevalue="" checked="false" label="full_tree"
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247 help="by default, we first compute the intersection of the tree with the otus present in the otu table. pass -f if you already have a minimal tree, and this script will run faster"/>
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248 </inputs>
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249 <outputs>
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250 <data format="qiimedistmat" name="binary_chisq" label="${tool.name} on ${on_string}: binary_chisq.dist">
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251 <filter>'binary_chisq' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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252 </data>
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253 <data format="qiimedistmat" name="binary_chord" label="${tool.name} on ${on_string}: binary_chord.dist">
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254 <filter>'binary_chord' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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255 </data>
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256 <data format="qiimedistmat" name="binary_euclidean" label="${tool.name} on ${on_string}: binary_euclidean.dist">
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257 <filter>'binary_euclidean' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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258 </data>
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259 <data format="qiimedistmat" name="binary_hamming" label="${tool.name} on ${on_string}: binary_hamming.dist">
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260 <filter>'binary_hamming' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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261 </data>
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262 <data format="qiimedistmat" name="binary_jaccard" label="${tool.name} on ${on_string}: binary_jaccard.dist">
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263 <filter>'binary_jaccard' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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264 </data>
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265 <data format="qiimedistmat" name="binary_lennon" label="${tool.name} on ${on_string}: binary_lennon.dist">
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266 <filter>'binary_lennon' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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267 </data>
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268 <data format="qiimedistmat" name="binary_ochiai" label="${tool.name} on ${on_string}: binary_ochiai.dist">
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269 <filter>'binary_ochiai' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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270 </data>
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271 <data format="qiimedistmat" name="binary_pearson" label="${tool.name} on ${on_string}: binary_pearson.dist">
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272 <filter>'binary_pearson' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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273 </data>
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274 <data format="qiimedistmat" name="binary_sorensen_dice" label="${tool.name} on ${on_string}: binary_sorensen_dice.dist">
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275 <filter>'binary_sorensen_dice' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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276 </data>
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277 <data format="qiimedistmat" name="bray_curtis" label="${tool.name} on ${on_string}: bray_curtis.dist">
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278 <filter>'bray_curtis' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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279 </data>
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280 <data format="qiimedistmat" name="canberra" label="${tool.name} on ${on_string}: canberra.dist">
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281 <filter>'canberra' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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282 </data>
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283 <data format="qiimedistmat" name="chisq" label="${tool.name} on ${on_string}: chisq.dist">
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284 <filter>'chisq' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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285 </data>
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286 <data format="qiimedistmat" name="chord" label="${tool.name} on ${on_string}: chord.dist">
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287 <filter>'chord' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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288 </data>
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289 <data format="qiimedistmat" name="euclidean" label="${tool.name} on ${on_string}: euclidean.dist">
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290 <filter>'euclidean' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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291 </data>
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292 <data format="qiimedistmat" name="gower" label="${tool.name} on ${on_string}: gower.dist">
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293 <filter>'gower' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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294 </data>
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295 <data format="qiimedistmat" name="hellinger" label="${tool.name} on ${on_string}: hellinger.dist">
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296 <filter>'hellinger' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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297 </data>
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298 <data format="qiimedistmat" name="kulczynski" label="${tool.name} on ${on_string}: kulczynski.dist">
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299 <filter>'kulczynski' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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300 </data>
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301 <data format="qiimedistmat" name="manhattan" label="${tool.name} on ${on_string}: manhattan.dist">
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302 <filter>'manhattan' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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303 </data>
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304 <data format="qiimedistmat" name="morisita_horn" label="${tool.name} on ${on_string}: morisita_horn.dist">
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305 <filter>'morisita_horn' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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306 </data>
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307 <data format="qiimedistmat" name="pearson" label="${tool.name} on ${on_string}: pearson.dist">
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308 <filter>'pearson' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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309 </data>
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310 <data format="qiimedistmat" name="soergel" label="${tool.name} on ${on_string}: soergel.dist">
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311 <filter>'soergel' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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312 </data>
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313 <data format="qiimedistmat" name="spearman_approx" label="${tool.name} on ${on_string}: spearman_approx.dist">
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314 <filter>'spearman_approx' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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315 </data>
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316 <data format="qiimedistmat" name="specprof" label="${tool.name} on ${on_string}: specprof.dist">
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317 <filter>'specprof' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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318 </data>
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319 <data format="qiimedistmat" name="unifrac" label="${tool.name} on ${on_string}: unifrac.dist">
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320 <filter>'unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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321 </data>
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322 <data format="qiimedistmat" name="unifrac_g" label="${tool.name} on ${on_string}: unifrac_g.dist">
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323 <filter>'unifrac_g' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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324 </data>
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325 <data format="qiimedistmat" name="unifrac_g_full_tree" label="${tool.name} on ${on_string}: unifrac_g_full_tree.dist">
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326 <filter>'unifrac_g_full_tree' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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327 </data>
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328 <data format="qiimedistmat" name="unweighted_unifrac" label="${tool.name} on ${on_string}: unweighted_unifrac.dist">
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329 <filter>'unweighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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330 </data>
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331 <data format="qiimedistmat" name="unweighted_unifrac_full_tree" label="${tool.name} on ${on_string}: unweighted_unifrac_full_tree.dist">
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332 <filter>'unweighted_unifrac_full_tree' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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333 </data>
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334 <data format="qiimedistmat" name="weighted_normalized_unifrac" label="${tool.name} on ${on_string}: weighted_normalized_unifrac.dist">
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335 <filter>'weighted_normalized_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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336 </data>
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337 <data format="qiimedistmat" name="weighted_unifrac" label="${tool.name} on ${on_string}: weighted_unifrac.dist">
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338 <filter>'weighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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339 </data>
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340 </outputs>
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341 <tests>
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342 </tests>
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343 <help>For more information, see beta_diversity_ in the Qiime documentation.
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344
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345 Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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346
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347 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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348
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349 .. _beta_diversity: http://qiime.org/scripts/beta_diversity.html</help>
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350 </tool>
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351
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