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