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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"
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3 version="2020.8">
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4 <description>Beta diversity rarefaction</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime diversity beta-rarefaction
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10
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11 --i-table=$itable
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12
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13 #if str($iphylogeny) != 'None':
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14 --i-phylogeny=$iphylogeny
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15 #end if
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16
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17 --p-metric=$pmetric
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18
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19 --p-clustering-method=$pclusteringmethod
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20 # if $input_files_mmetadatafile:
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21 # def list_dict_to_string(list_dict):
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22 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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23 # for d in list_dict[1:]:
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24 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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25 # end for
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26 # return $file_list
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27 # end def
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28 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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29 # end if
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30
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31 --p-sampling-depth=$psamplingdepth
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32
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33 --p-iterations=$piterations
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34
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35 #if str($pcorrelationmethod) != 'None':
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36 --p-correlation-method=$pcorrelationmethod
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37 #end if
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38
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39 #if str($pcolorscheme) != 'None':
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40 --p-color-scheme=$pcolorscheme
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41 #end if
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42
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43 --o-visualization=ovisualization
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44
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45 #if str($examples) != 'None':
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46 --examples=$examples
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47 #end if
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48
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49 ;
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50 cp odistancematrix.qza $odistancematrix
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51
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52 ;
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53 qiime tools export ovisualization.qzv --output-path out
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54 && mkdir -p '$ovisualization.files_path'
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55 && cp -r out/* '$ovisualization.files_path'
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56 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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57
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58 ]]></command>
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59 <inputs>
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60 <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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61 <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="False" type="data" />
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62 <param label="--p-metric: " name="pmetric" optional="False" type="select">
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63 <option value="braycurtis">braycurtis</option>
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64 <option value="euclidean">euclidean</option>
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65 <option value="cityblock">cityblock</option>
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66 <option value="cosine">cosine</option>
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67 <option value="minkowski">minkowski</option>
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68 <option value="matching">matching</option>
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69 <option value="correlation">correlation</option>
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70 <option value="russellrao">russellrao</option>
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71 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
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72 <option value="sokalsneath">sokalsneath</option>
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73 <option value="seuclidean">seuclidean</option>
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74 <option value="canberra">canberra</option>
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75 <option value="sokalmichener">sokalmichener</option>
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76 <option value="kulsinski">kulsinski</option>
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77 <option value="jensenshannon">jensenshannon</option>
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78 <option value="weighted_unifrac">weighted_unifrac</option>
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79 <option value="jaccard">jaccard</option>
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80 <option value="hamming">hamming</option>
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81 <option value="chebyshev">chebyshev</option>
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82 <option value="generalized_unifrac">generalized_unifrac</option>
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83 <option value="yule">yule</option>
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84 <option value="dice">dice</option>
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85 <option value="sqeuclidean">sqeuclidean</option>
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86 <option value="aitchison">aitchison</option>
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87 <option value="canberra_adkins">canberra_adkins</option>
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88 <option value="unweighted_unifrac">unweighted_unifrac</option>
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89 <option value="rogerstanimoto">rogerstanimoto</option>
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90 </param>
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91 <param label="--p-clustering-method: " name="pclusteringmethod" optional="False" type="select">
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92 <option value="upgma">upgma</option>
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93 <option value="nj">nj</option>
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94 </param>
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95 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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96 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments The sample metadata used for the Emperor jackknifed will be merged) PCoA plot. [required]" name="additional_input" optional="False" type="data" />
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97 </repeat>
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98 <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" type="text" />
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99 <param label="--p-iterations: INTEGER Number of times to rarefy the feature table at a Range(2, None) given sampling depth. [default: 10]" min="2" name="piterations" optional="True" type="integer" value="10" />
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100 <param label="--p-correlation-method: " name="pcorrelationmethod" optional="True" type="select">
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101 <option selected="True" value="None">Selection is Optional</option>
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102 <option value="pearson">pearson</option>
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103 <option value="spearman">spearman</option>
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104 </param>
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105 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
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106 <option selected="True" value="None">Selection is Optional</option>
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107 <option value="BrBG">BrBG</option>
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108 <option value="BrBG_r">BrBG_r</option>
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109 <option value="PRGn">PRGn</option>
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110 <option value="PRGn_r">PRGn_r</option>
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111 <option value="PiYG">PiYG</option>
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112 <option value="PiYG_r">PiYG_r</option>
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113 <option value="PuOr">PuOr</option>
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114 <option value="PuOr_r">PuOr_r</option>
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115 <option value="RdBu">RdBu</option>
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116 <option value="RdBu_r">RdBu_r</option>
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117 <option value="RdGy">RdGy</option>
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118 <option value="RdGy_r">RdGy_r</option>
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119 <option value="RdYlBu">RdYlBu</option>
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120 <option value="RdYlBu_r">RdYlBu_r</option>
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121 <option value="RdYlGn">RdYlGn</option>
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122 <option value="RdYlGn_r">RdYlGn_r</option>
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123 </param>
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124 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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125
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126 </inputs>
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127
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128 <outputs>
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129 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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130
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131 </outputs>
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132
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133 <help><![CDATA[
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134 Beta diversity rarefaction
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135 ###############################################################
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136
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137 Repeatedly rarefy a feature table to compare beta diversity results within
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138 a given rarefaction depth. For a given beta diversity metric, this
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139 visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered
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140 by UPGMA or neighbor joining with support calculation, and a heatmap
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141 showing the correlation between rarefaction trials of that beta diversity
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142 metric.
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143
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144 Parameters
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145 ----------
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146 table : FeatureTable[Frequency]
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147 Feature table upon which to perform beta diversity rarefaction
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148 analyses.
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149 metric : Str % Choices('yule', 'weighted_normalized_unifrac', 'cityblock', 'weighted_unifrac', 'matching', 'russellrao', 'seuclidean', 'jaccard', 'braycurtis', 'minkowski', 'sokalmichener', 'aitchison', 'generalized_unifrac', 'canberra_adkins', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'sokalsneath', 'correlation', 'hamming', 'dice', 'rogerstanimoto', 'canberra', 'unweighted_unifrac', 'chebyshev', 'jensenshannon')
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150 The beta diversity metric to be computed.
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151 clustering_method : Str % Choices('upgma', 'nj')
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152 Samples can be clustered with neighbor joining or UPGMA. An arbitrary
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153 rarefaction trial will be used for the tree, and the remaining trials
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154 are used to calculate the support of the internal nodes of that tree.
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155 metadata : Metadata
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156 The sample metadata used for the Emperor jackknifed PCoA plot.
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157 sampling_depth : Int % Range(1, None)
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158 The total frequency that each sample should be rarefied to prior to
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159 computing the diversity metric.
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160 iterations : Int % Range(2, None), optional
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161 Number of times to rarefy the feature table at a given sampling depth.
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162 phylogeny : Phylogeny[Rooted], optional
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163 Phylogenetic tree containing tip identifiers that correspond to the
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164 feature identifiers in the table. This tree can contain tip ids that
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165 are not present in the table, but all feature ids in the table must be
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166 present in this tree. [required for phylogenetic metrics]
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167 correlation_method : Str % Choices('spearman', 'pearson'), optional
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168 The Mantel correlation test to be applied when computing correlation
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169 between beta diversity distance matrices.
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170 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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171 The matplotlib color scheme to generate the heatmap with.
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172
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173 Returns
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174 -------
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175 visualization : Visualization
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176 ]]></help>
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177 <macros>
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178 <import>qiime_citation.xml</import>
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179 </macros>
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180 <expand macro="qiime_citation"/>
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181 </tool> |
