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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="2019.4">
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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="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity beta-rarefaction
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9
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10 --i-table=$itable
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6
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11
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12 --p-metric=$pmetric
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6
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13
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14 --p-clustering-method=$pclusteringmethod
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6
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15
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16 #if str($psamplingdepth):
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17 --p-sampling-depth="$psamplingdepth"
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18 #end if
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19
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20 #if str($iphylogeny) != 'None':
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21 --i-phylogeny=$iphylogeny
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22 #end if
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23
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6
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24 #if str($piterations):
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25 --p-iterations=$piterations
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26 #end if
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27
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28 #if str($pcorrelationmethod) != 'None':
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29 --p-correlation-method=$pcorrelationmethod
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30 #end if
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31
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32 #if str($pcolorscheme) != 'None':
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33 --p-color-scheme=$pcolorscheme
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34 #end if
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35
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2
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36 #if $input_files_mmetadatafile:
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37 #def list_dict_to_string(list_dict):
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38 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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39 #for d in list_dict[1:]:
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4
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40 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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41 #end for
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42 #return $file_list
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43 #end def
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44 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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2
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45 #end if
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0
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46
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47 --o-visualization=ovisualization
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48 ;
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49 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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50 && cp -r out/* '$ovisualization.files_path'
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51 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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52 ]]></command>
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53 <inputs>
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54 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table upon which to perform beta diversity rarefaction analyses. [required]" name="itable" optional="False" type="data"/>
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55 <param label="--p-metric: " name="pmetric" optional="False" type="select">
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56 <option value="kulsinski">kulsinski</option>
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57 <option value="euclidean">euclidean</option>
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58 <option value="wminkowski">wminkowski</option>
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59 <option value="dice">dice</option>
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60 <option value="correlation">correlation</option>
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61 <option value="hamming">hamming</option>
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62 <option value="canberra">canberra</option>
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63 <option value="canberra_adkins">canberra_adkins</option>
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64 <option value="rogerstanimoto">rogerstanimoto</option>
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65 <option value="sqeuclidean">sqeuclidean</option>
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66 <option value="cosine">cosine</option>
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67 <option value="seuclidean">seuclidean</option>
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68 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
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69 <option value="sokalmichener">sokalmichener</option>
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70 <option value="unweighted_unifrac">unweighted_unifrac</option>
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71 <option value="cityblock">cityblock</option>
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72 <option value="generalized_unifrac">generalized_unifrac</option>
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73 <option value="weighted_unifrac">weighted_unifrac</option>
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74 <option value="braycurtis">braycurtis</option>
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75 <option value="jaccard">jaccard</option>
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76 <option value="sokalsneath">sokalsneath</option>
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77 <option value="aitchison">aitchison</option>
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78 <option value="matching">matching</option>
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79 <option value="chebyshev">chebyshev</option>
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80 <option value="russellrao">russellrao</option>
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81 <option value="yule">yule</option>
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82 <option value="mahalanobis">mahalanobis</option>
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83 </param>
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84 <param label="--p-clustering-method: " name="pclusteringmethod" optional="False" type="select">
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85 <option value="upgma">upgma</option>
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86 <option value="nj">nj</option>
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87 </param>
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88 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing the diversity metric. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>
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89 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] 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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90 <param label="--p-iterations: INTEGER Number of times to rarefy the feature table at a Range(2, None) given sampling depth. [default: 10]" name="piterations" optional="True" type="integer" min="2" value="10"/>
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91 <param label="--p-correlation-method: " name="pcorrelationmethod" optional="True" type="select">
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92 <option selected="True" value="None">Selection is Optional</option>
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93 <option value="spearman">spearman</option>
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94 <option value="pearson">pearson</option>
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95 </param>
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96 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
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97 <option selected="True" value="None">Selection is Optional</option>
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98 <option value="BrBG">BrBG</option>
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99 <option value="BrBG_r">BrBG_r</option>
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100 <option value="PRGn">PRGn</option>
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101 <option value="PRGn_r">PRGn_r</option>
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102 <option value="PiYG">PiYG</option>
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103 <option value="PiYG_r">PiYG_r</option>
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104 <option value="PuOr">PuOr</option>
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105 <option value="PuOr_r">PuOr_r</option>
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106 <option value="RdBu">RdBu</option>
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107 <option value="RdBu_r">RdBu_r</option>
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108 <option value="RdGy">RdGy</option>
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109 <option value="RdGy_r">RdGy_r</option>
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110 <option value="RdYlBu">RdYlBu</option>
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111 <option value="RdYlBu_r">RdYlBu_r</option>
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112 <option value="RdYlGn">RdYlGn</option>
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113 <option value="RdYlGn_r">RdYlGn_r</option>
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114 </param>
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115
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116 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
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117 <param label="--m-metadata-file: METADATA... (multiple arguments will be merged) 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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118 </repeat>
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119
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120 </inputs>
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121 <outputs>
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122 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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123 </outputs>
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124 <help><![CDATA[
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125 Beta diversity rarefaction
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126 ##########################
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127
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128 Repeatedly rarefy a feature table to compare beta diversity results within
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129 a given rarefaction depth. For a given beta diversity metric, this
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130 visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered
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131 by UPGMA or neighbor joining with support calculation, and a heatmap
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132 showing the correlation between rarefaction trials of that beta diversity
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133 metric.
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134
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135 Parameters
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136 ----------
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137 table : FeatureTable[Frequency]
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138 Feature table upon which to perform beta diversity rarefaction
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139 analyses.
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140 metric : Str % Choices('generalized_unifrac', 'sokalmichener', 'matching', 'yule', 'weighted_normalized_unifrac', 'dice', 'russellrao', 'rogerstanimoto', 'mahalanobis', 'wminkowski', 'kulsinski', 'aitchison', 'seuclidean', 'correlation', 'sokalsneath', 'hamming', 'jaccard', 'unweighted_unifrac', 'weighted_unifrac', 'cosine', 'canberra', 'euclidean', 'sqeuclidean', 'chebyshev', 'cityblock', 'canberra_adkins', 'braycurtis')
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141 The beta diversity metric to be computed.
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142 clustering_method : Str % Choices('upgma', 'nj')
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143 Samples can be clustered with neighbor joining or UPGMA. An arbitrary
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144 rarefaction trial will be used for the tree, and the remaining trials
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145 are used to calculate the support of the internal nodes of that tree.
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146 metadata : Metadata
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147 The sample metadata used for the Emperor jackknifed PCoA plot.
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148 sampling_depth : Int % Range(1, None)
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149 The total frequency that each sample should be rarefied to prior to
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150 computing the diversity metric.
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151 iterations : Int % Range(2, None), optional
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152 Number of times to rarefy the feature table at a given sampling depth.
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153 phylogeny : Phylogeny[Rooted], optional
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154 Phylogenetic tree containing tip identifiers that correspond to the
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155 feature identifiers in the table. This tree can contain tip ids that
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156 are not present in the table, but all feature ids in the table must be
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157 present in this tree. [required for phylogenetic metrics]
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158 correlation_method : Str % Choices('pearson', 'spearman'), optional
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159 The Mantel correlation test to be applied when computing correlation
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160 between beta diversity distance matrices.
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161 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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162 The matplotlib color scheme to generate the heatmap with.
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163
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164 Returns
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165 -------
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166 visualization : Visualization
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167 ]]></help>
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168 <macros>
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169 <import>qiime_citation.xml</import>
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170 </macros>
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171 <expand macro="qiime_citation"/>
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172 </tool>
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