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