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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="beta_diversity" name="beta_diversity" version="1.2.0">
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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_tmpdir='$__new_file_path__'
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9 #set datasets = []
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10 #if $binary_chisq.__str__ != "None":
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11 #set datasets = $datasets + ["'binary_chisq_.*$:'" + $binary_chisq.__str__]
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12 #end if
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13 #if $binary_chord.__str__ != "None":
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14 #set datasets = $datasets + ["'binary_chord_.*$:'" + $binary_chord.__str__]
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15 #end if
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16 #if $binary_euclidean.__str__ != "None":
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17 #set datasets = $datasets + ["'binary_euclidean_.*$:'" + $binary_euclidean.__str__]
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18 #end if
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19 #if $binary_hamming.__str__ != "None":
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20 #set datasets = $datasets + ["'binary_hamming_.*$:'" + $binary_hamming.__str__]
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21 #end if
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22 #if $binary_jaccard.__str__ != "None":
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23 #set datasets = $datasets + ["'binary_jaccard_.*$:'" + $binary_jaccard.__str__]
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24 #end if
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25 #if $binary_lennon.__str__ != "None":
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26 #set datasets = $datasets + ["'binary_lennon_.*$:'" + $binary_lennon.__str__]
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27 #end if
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28 #if $binary_ochiai.__str__ != "None":
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29 #set datasets = $datasets + ["'binary_ochiai_.*$:'" + $binary_ochiai.__str__]
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30 #end if
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31 #if $binary_pearson.__str__ != "None":
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32 #set datasets = $datasets + ["'binary_pearson_.*$:'" + $binary_pearson.__str__]
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33 #end if
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34 #if $binary_sorensen_dice.__str__ != "None":
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35 #set datasets = $datasets + ["'binary_sorensen_dice_.*$:'" + $binary_sorensen_dice.__str__]
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36 #end if
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37 #if $bray_curtis.__str__ != "None":
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38 #set datasets = $datasets + ["'bray_curtis_.*$:'" + $bray_curtis.__str__]
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39 #end if
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40 #if $canberra.__str__ != "None":
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41 #set datasets = $datasets + ["'canberra_.*$:'" + $canberra.__str__]
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42 #end if
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43 #if $chisq.__str__ != "None":
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44 #set datasets = $datasets + ["'chisq_.*$:'" + $chisq.__str__]
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45 #end if
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46 #if $chord.__str__ != "None":
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47 #set datasets = $datasets + ["'chord_.*$:'" + $chord.__str__]
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48 #end if
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49 #if $euclidean.__str__ != "None":
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50 #set datasets = $datasets + ["'euclidean_.*$:'" + $euclidean.__str__]
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51 #end if
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52 #if $gower.__str__ != "None":
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53 #set datasets = $datasets + ["'gower_.*$:'" + $gower.__str__]
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54 #end if
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55 #if $hellinger.__str__ != "None":
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56 #set datasets = $datasets + ["'hellinger_.*$:'" + $hellinger.__str__]
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57 #end if
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58 #if $kulczynski.__str__ != "None":
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59 #set datasets = $datasets + ["'kulczynski_.*$:'" + $kulczynski.__str__]
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60 #end if
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61 #if $manhattan.__str__ != "None":
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62 #set datasets = $datasets + ["'manhattan_.*$:'" + $manhattan.__str__]
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63 #end if
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64 #if $morisita_horn.__str__ != "None":
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65 #set datasets = $datasets + ["'morisita_horn_.*$:'" + $morisita_horn.__str__]
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66 #end if
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67 #if $pearson.__str__ != "None":
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68 #set datasets = $datasets + ["'pearson_.*$:'" + $pearson.__str__]
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69 #end if
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70 #if $soergel.__str__ != "None":
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71 #set datasets = $datasets + ["'soergel_.*$:'" + $soergel.__str__]
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72 #end if
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73 #if $spearman_approx.__str__ != "None":
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74 #set datasets = $datasets + ["'spearman_approx_.*$:'" + $spearman_approx.__str__]
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75 #end if
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76 #if $specprof.__str__ != "None":
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77 #set datasets = $datasets + ["'specprof_.*$:'" + $specprof.__str__]
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78 #end if
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79 #if $unifrac.__str__ != "None":
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80 #set datasets = $datasets + ["'unifrac_.*$:'" + $unifrac.__str__]
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81 #end if
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82 #if $unifrac_g.__str__ != "None":
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83 #set datasets = $datasets + ["'unifrac_g_.*$:'" + $unifrac_g.__str__]
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84 #end if
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85 #if $unifrac_g_full_tree.__str__ != "None":
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86 #set datasets = $datasets + ["'unifrac_g_full_tree_.*$:'" + $unifrac_g_full_tree.__str__]
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87 #end if
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88 #if $unweighted_unifrac.__str__ != "None":
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89 #set datasets = $datasets + ["'unweighted_unifrac_.*$:'" + $unweighted_unifrac.__str__]
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90 #end if
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91 #if $unweighted_unifrac_full_tree.__str__ != "None":
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92 #set datasets = $datasets + ["'unweighted_unifrac_full_tree_.*$:'" + $unweighted_unifrac_full_tree.__str__]
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93 #end if
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94 #if $weighted_normalized_unifrac.__str__ != "None":
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95 #set datasets = $datasets + ["'weighted_normalized_unifrac_.*$:'" + $weighted_normalized_unifrac.__str__]
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96 #end if
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97 #if $weighted_unifrac.__str__ != "None":
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98 #set datasets = $datasets + ["'weighted_unifrac_.*$:'" + $weighted_unifrac.__str__]
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99 #end if
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100 --galaxy_datasets=#echo ','.join($datasets)
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101 beta_diversity.py
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102 --input_path=$input_path
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103 #if $rows.__str__ != '':
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104 --rows=$rows
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105 #end if
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106 --output_dir=$__new_file_path__
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107 --metrics=$metrics
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108 #if $tree_path.__str__ != "None" and len($tree_path.__str__) > 0:
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109 --tree_path=$tree_path
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110 #end if
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111 $full_tree
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112 </command>
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113 <inputs>
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114 <param name="input_path" type="data" format="qiimeotutable" label="input_path"
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115 help="input path: otu table"/>
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116 <param name="rows" type="text" label="rows"
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117 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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118 <param name="metrics" type="select" multiple="true" label="metrics" help="metrics to use">
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119 <option value="abund_jaccard">abund_jaccard</option>
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120 <option value="binary_chisq">binary_chisq</option>
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121 <option value="binary_chord">binary_chord</option>
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122 <option value="binary_euclidean">binary_euclidean</option>
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123 <option value="binary_hamming">binary_hamming</option>
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124 <option value="binary_jaccard">binary_jaccard</option>
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125 <option value="binary_lennon">binary_lennon</option>
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126 <option value="binary_ochiai">binary_ochiai</option>
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127 <option value="binary_otu_gain">binary_otu_gain</option>
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128 <option value="binary_pearson">binary_pearson</option>
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129 <option value="binary_sorensen_dice">binary_sorensen_dice</option>
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130 <option value="bray_curtis">bray_curtis</option>
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131 <option value="canberra">canberra</option>
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132 <option value="chisq">chisq</option>
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133 <option value="chord">chord</option>
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134 <option value="euclidean">euclidean</option>
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135 <option value="gower">gower</option>
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136 <option value="hellinger">hellinger</option>
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137 <option value="kulczynski">kulczynski</option>
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138 <option value="manhattan">manhattan</option>
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139 <option value="morisita_horn">morisita_horn</option>
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140 <option value="pearson">pearson</option>
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141 <option value="soergel">soergel</option>
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142 <option value="spearman_approx">spearman_approx</option>
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143 <option value="specprof">specprof</option>
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144 <option value="unifrac">unifrac</option>
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145 <option value="unifrac_g">unifrac_g</option>
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146 <option value="unifrac_g_full_tree">unifrac_g_full_tree</option>
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147 <option value="unweighted_unifrac">unweighted_unifrac</option>
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148 <option value="unweighted_unifrac_full_tree">unweighted_unifrac_full_tree</option>
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149 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
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150 <option value="weighted_unifrac">weighted_unifrac</option>
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151 </param>
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152 <param name="tree_path" type="text" label="tree_path"
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153 help="path to newick tree file, required for phylogenetic metrics [default: %default]"/>
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154 <param name="full_tree" type="boolean" truevalue="--full_tree" falsevalue="" checked="false" label="full_tree"
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155 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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156 </inputs>
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157 <outputs>
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158 <data format="qiimedistmat" name="binary_chisq" label="${tool.name} on ${on_string}: binary_chisq.dist">
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159 <filter>'binary_chisq' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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160 </data>
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161 <data format="qiimedistmat" name="binary_chord" label="${tool.name} on ${on_string}: binary_chord.dist">
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162 <filter>'binary_chord' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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163 </data>
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164 <data format="qiimedistmat" name="binary_euclidean" label="${tool.name} on ${on_string}: binary_euclidean.dist">
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165 <filter>'binary_euclidean' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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166 </data>
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167 <data format="qiimedistmat" name="binary_hamming" label="${tool.name} on ${on_string}: binary_hamming.dist">
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168 <filter>'binary_hamming' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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169 </data>
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170 <data format="qiimedistmat" name="binary_jaccard" label="${tool.name} on ${on_string}: binary_jaccard.dist">
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171 <filter>'binary_jaccard' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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172 </data>
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173 <data format="qiimedistmat" name="binary_lennon" label="${tool.name} on ${on_string}: binary_lennon.dist">
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174 <filter>'binary_lennon' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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175 </data>
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176 <data format="qiimedistmat" name="binary_ochiai" label="${tool.name} on ${on_string}: binary_ochiai.dist">
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177 <filter>'binary_ochiai' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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178 </data>
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179 <data format="qiimedistmat" name="binary_pearson" label="${tool.name} on ${on_string}: binary_pearson.dist">
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180 <filter>'binary_pearson' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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181 </data>
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182 <data format="qiimedistmat" name="binary_sorensen_dice" label="${tool.name} on ${on_string}: binary_sorensen_dice.dist">
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183 <filter>'binary_sorensen_dice' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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184 </data>
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185 <data format="qiimedistmat" name="bray_curtis" label="${tool.name} on ${on_string}: bray_curtis.dist">
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186 <filter>'bray_curtis' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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187 </data>
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188 <data format="qiimedistmat" name="canberra" label="${tool.name} on ${on_string}: canberra.dist">
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189 <filter>'canberra' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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190 </data>
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191 <data format="qiimedistmat" name="chisq" label="${tool.name} on ${on_string}: chisq.dist">
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192 <filter>'chisq' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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193 </data>
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194 <data format="qiimedistmat" name="chord" label="${tool.name} on ${on_string}: chord.dist">
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195 <filter>'chord' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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196 </data>
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197 <data format="qiimedistmat" name="euclidean" label="${tool.name} on ${on_string}: euclidean.dist">
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198 <filter>'euclidean' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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199 </data>
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200 <data format="qiimedistmat" name="gower" label="${tool.name} on ${on_string}: gower.dist">
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201 <filter>'gower' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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202 </data>
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203 <data format="qiimedistmat" name="hellinger" label="${tool.name} on ${on_string}: hellinger.dist">
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204 <filter>'hellinger' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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205 </data>
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206 <data format="qiimedistmat" name="kulczynski" label="${tool.name} on ${on_string}: kulczynski.dist">
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207 <filter>'kulczynski' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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208 </data>
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209 <data format="qiimedistmat" name="manhattan" label="${tool.name} on ${on_string}: manhattan.dist">
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210 <filter>'manhattan' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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211 </data>
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212 <data format="qiimedistmat" name="morisita_horn" label="${tool.name} on ${on_string}: morisita_horn.dist">
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213 <filter>'morisita_horn' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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214 </data>
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215 <data format="qiimedistmat" name="pearson" label="${tool.name} on ${on_string}: pearson.dist">
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216 <filter>'pearson' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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217 </data>
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218 <data format="qiimedistmat" name="soergel" label="${tool.name} on ${on_string}: soergel.dist">
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219 <filter>'soergel' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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220 </data>
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221 <data format="qiimedistmat" name="spearman_approx" label="${tool.name} on ${on_string}: spearman_approx.dist">
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222 <filter>'spearman_approx' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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223 </data>
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224 <data format="qiimedistmat" name="specprof" label="${tool.name} on ${on_string}: specprof.dist">
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225 <filter>'specprof' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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226 </data>
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227 <data format="qiimedistmat" name="unifrac" label="${tool.name} on ${on_string}: unifrac.dist">
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228 <filter>'unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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229 </data>
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230 <data format="qiimedistmat" name="unifrac_g" label="${tool.name} on ${on_string}: unifrac_g.dist">
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231 <filter>'unifrac_g' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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232 </data>
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233 <data format="qiimedistmat" name="unifrac_g_full_tree" label="${tool.name} on ${on_string}: unifrac_g_full_tree.dist">
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234 <filter>'unifrac_g_full_tree' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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235 </data>
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236 <data format="qiimedistmat" name="unweighted_unifrac" label="${tool.name} on ${on_string}: unweighted_unifrac.dist">
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237 <filter>'unweighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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238 </data>
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239 <data format="qiimedistmat" name="unweighted_unifrac_full_tree" label="${tool.name} on ${on_string}: unweighted_unifrac_full_tree.dist">
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240 <filter>'unweighted_unifrac_full_tree' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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241 </data>
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242 <data format="qiimedistmat" name="weighted_normalized_unifrac" label="${tool.name} on ${on_string}: weighted_normalized_unifrac.dist">
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243 <filter>'weighted_normalized_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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244 </data>
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245 <data format="qiimedistmat" name="weighted_unifrac" label="${tool.name} on ${on_string}: weighted_unifrac.dist">
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246 <filter>'weighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
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247 </data>
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248 </outputs>
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249 <tests>
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250 </tests>
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251 <help>
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252
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253 </help>
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254 </tool>
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255