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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_beta-rarefaction" name="qiime diversity beta-rarefaction" version="2018.4">
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3 <description> - Beta diversity rarefaction</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity beta-rarefaction --i-table=$itable
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9
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10 #def list_dict_to_string(list_dict):
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11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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12 #for d in list_dict[1:]:
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13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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14 #end for
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15 #return $file_list
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16 #end def
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17
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18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-clustering-method=$pclusteringmethod --p-metric=$pmetric --p-sampling-depth="$psamplingdepth"
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19
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20 #if str($pcorrelationmethod) != 'None':
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21 --p-correlation-method=$pcorrelationmethod
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22 #end if
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23
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24 #if str($pcolorscheme) != 'None':
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25 --p-color-scheme=$pcolorscheme
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26 #end if
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27
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28 --o-visualization=ovisualization
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29
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30 #if str($cmdconfig) != 'None':
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31 --cmd-config=$cmdconfig
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32 #end if
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33
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34 #if str($iphylogeny) != 'None':
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35 --i-phylogeny=$iphylogeny
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36 #end if
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37
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38 #if $piterations:
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39 --p-iterations=$piterations
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40 #end if
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41 ;
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42 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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43 && cp -r out/* '$ovisualization.files_path'
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44 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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45 ]]></command>
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46 <inputs>
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47 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table upon which to perform beta diversity rarefaction analyses. [required]" name="itable" optional="False" type="data"/>
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48 <param format="qza,no_unzip.zip" label="--i-phylogeny: Phylogeny[Rooted] Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required for phylogenetic metrics] [optional]" name="iphylogeny" optional="True" type="data"/>
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49
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50 <param label="--p-metric: The beta diversity metric to be computed.
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51 [required]" name="pmetric" optional="False" type="select">
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52 <option value="hamming">hamming</option>
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53 <option value="sqeuclidean">sqeuclidean</option>
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54 <option value="cityblock">cityblock</option>
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55 <option value="sokalmichener">sokalmichener</option>
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56 <option value="braycurtis">braycurtis</option>
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57 <option value="cosine">cosine</option>
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58 <option value="euclidean">euclidean</option>
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59 <option value="rogerstanimoto">rogerstanimoto</option>
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60 <option value="weighted_unifrac">weighted_unifrac</option>
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61 <option value="canberra">canberra</option>
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62 <option value="seuclidean">seuclidean</option>
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63 <option value="correlation">correlation</option>
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64 <option value="unweighted_unifrac">unweighted_unifrac</option>
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65 <option value="sokalsneath">sokalsneath</option>
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66 <option value="chebyshev">chebyshev</option>
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67 <option value="mahalanobis">mahalanobis</option>
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68 <option value="matching">matching</option>
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69 <option value="kulsinski">kulsinski</option>
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70 <option value="yule">yule</option>
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71 <option value="dice">dice</option>
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72 <option value="russellrao">russellrao</option>
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73 <option value="wminkowski">wminkowski</option>
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74 <option value="jaccard">jaccard</option>
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75 </param>
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76 <param label="--p-clustering-method: Samples can be clustered with neighbor
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77 joining or UPGMA. An arbitrary rarefaction
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78 trial will be used for the tree, and the
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79 remaining trials are used to calculate the
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80 support of the internal nodes of that tree.
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81 [required]" name="pclusteringmethod" optional="False" type="select">
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82 <option value="upgma">upgma</option>
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83 <option value="nj">nj</option>
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84 </param>
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85
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86 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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87 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata used for the Emperor jackknifed PCoA plot. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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88 </repeat>
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89
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90 <param label="--p-sampling-depth: The total frequency that each sample should be rarefied to prior to computing the diversity metric. [required]" name="psamplingdepth" optional="False" type="text"/>
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91 <param label="--p-iterations: Number of times to rarefy the feature table at a given sampling depth. [default: 10]" name="piterations" optional="True" type="integer" value="10"/>
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92
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93 <param label="--p-correlation-method: The Mantel correlation test to be applied
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94 when computing correlation between beta
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95 diversity distance matrices. [default:
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96 spearman]" name="pcorrelationmethod" optional="True" type="select">
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97 <option selected="True" value="spearman">spearman</option>
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98 <option value="pearson">pearson</option>
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99 </param>
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100
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101 <param label="--p-color-scheme: The matplotlib color scheme to generate the
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102 heatmap with. [default: BrBG]" name="pcolorscheme" optional="True" type="select">
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103 <option value="PiYG">PiYG</option>
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104 <option value="RdYlGn_r">RdYlGn_r</option>
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105 <option value="RdYlBu_r">RdYlBu_r</option>
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106 <option value="RdYlGn">RdYlGn</option>
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107 <option value="BrBG_r">BrBG_r</option>
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108 <option value="RdYlBu">RdYlBu</option>
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109 <option value="RdGy">RdGy</option>
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110 <option value="PuOr">PuOr</option>
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111 <option value="RdBu_r">RdBu_r</option>
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112 <option value="RdGy_r">RdGy_r</option>
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113 <option value="PiYG_r">PiYG_r</option>
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114 <option value="RdBu">RdBu</option>
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115 <option value="PuOr_r">PuOr_r</option>
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116 <option value="PRGn">PRGn</option>
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117 <option selected="True" value="BrBG">BrBG</option>
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118 <option value="PRGn_r">PRGn_r</option>
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119 </param>
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120
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121 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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122 </inputs>
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123 <outputs>
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124 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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125 </outputs>
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126 <help><![CDATA[
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127 Beta diversity rarefaction
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128 --------------------------
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129
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130 Repeatedly rarefy a feature table to compare beta diversity results within
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131 a given rarefaction depth. For a given beta diversity metric, this
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132 visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered
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133 by UPGMA or neighbor joining with support calculation, and a heatmap
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134 showing the correlation between rarefaction trials of that beta diversity
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135 metric.
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136
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137 Parameters
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138 ----------
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139 table : FeatureTable[Frequency]
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140 Feature table upon which to perform beta diversity rarefaction
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141 analyses.
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142 phylogeny : Phylogeny[Rooted], optional
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143 Phylogenetic tree containing tip identifiers that correspond to the
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144 feature identifiers in the table. This tree can contain tip ids that
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145 are not present in the table, but all feature ids in the table must be
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146 present in this tree. [required for phylogenetic metrics]
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147 metric : Str % Choices({'braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'unweighted_unifrac', 'weighted_unifrac', 'wminkowski', 'yule'})
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148 The beta diversity metric to be computed.
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149 clustering_method : Str % Choices({'nj', 'upgma'})
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150 Samples can be clustered with neighbor joining or UPGMA. An arbitrary
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151 rarefaction trial will be used for the tree, and the remaining trials
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152 are used to calculate the support of the internal nodes of that tree.
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153 metadata : Metadata
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154 The sample metadata used for the Emperor jackknifed PCoA plot.
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155 sampling_depth : Int % Range(1, None)
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156 The total frequency that each sample should be rarefied to prior to
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157 computing the diversity metric.
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158 iterations : Int % Range(2, None), optional
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159 Number of times to rarefy the feature table at a given sampling depth.
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160 correlation_method : Str % Choices({'pearson', 'spearman'}), optional
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161 The Mantel correlation test to be applied when computing correlation
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162 between beta diversity distance matrices.
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163 color_scheme : Str % Choices({'BrBG', 'BrBG_r', 'PRGn', 'PRGn_r', 'PiYG', 'PiYG_r', 'PuOr', 'PuOr_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r'}), optional
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164 The matplotlib color scheme to generate the heatmap with.
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165
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166 Returns
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167 -------
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168 visualization : Visualization
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169 \
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170 ]]>
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171 </help>
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172 </tool>
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