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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_core-metrics" name="qiime diversity core-metrics"
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3 version="2020.8">
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4 <description>Core diversity metrics (non-phylogenetic)</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 core-metrics
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10
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11 --i-table=$itable
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12
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13 --p-sampling-depth=$psamplingdepth
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14 # if $input_files_mmetadatafile:
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15 # def list_dict_to_string(list_dict):
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16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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17 # for d in list_dict[1:]:
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18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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19 # end for
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20 # return $file_list
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21 # end def
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22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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23 # end if
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24
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25 #if $pwithreplacement:
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26 --p-with-replacement
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27 #end if
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28
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29 #if str($pnjobs) != 'None':
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30 --p-n-jobs=$pnjobs
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31 #end if
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32
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33 --o-rarefied-table=orarefiedtable
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34
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35 --o-observed-features-vector=oobservedfeaturesvector
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36
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37 --o-shannon-vector=oshannonvector
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38
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39 --o-evenness-vector=oevennessvector
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40
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41 --o-jaccard-distance-matrix=ojaccarddistancematrix
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42
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43 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
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44
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45 --o-jaccard-pcoa-results=ojaccardpcoaresults
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46
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47 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
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48
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49 --o-jaccard-emperor=ojaccardemperor
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50
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51 --o-bray-curtis-emperor=obraycurtisemperor
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52
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53 #if str($examples) != 'None':
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54 --examples=$examples
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55 #end if
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56
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57 ;
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58 cp obraycurtispcoaresults.qza $obraycurtispcoaresults
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59
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60 ;
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61 qiime tools export ojaccardemperor.qzv --output-path out
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62 && mkdir -p '$ojaccardemperor.files_path'
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63 && cp -r out/* '$ojaccardemperor.files_path'
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64 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor'
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65
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66 ;
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67 qiime tools export obraycurtisemperor.qzv --output-path out
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68 && mkdir -p '$obraycurtisemperor.files_path'
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69 && cp -r out/* '$obraycurtisemperor.files_path'
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70 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor'
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71
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72 ]]></command>
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73 <inputs>
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74 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data" />
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75 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" type="text" />
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76 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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77 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata to use in the emperor plots. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
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78 </repeat>
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79 <param label="--p-with-replacement: --p-with-replacement: / --p-no-with-replacement Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement. [default: False]" name="pwithreplacement" selected="False" type="boolean" />
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80 <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
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81 <option selected="True" value="None">Selection is Optional</option>
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82 <option value="Int % Range(1">Int % Range(1</option>
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83 <option value="None">None</option>
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84 </param>
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85 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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86
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87 </inputs>
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88
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89 <outputs>
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90 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable" />
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91 <data format="qza" label="${tool.name} on ${on_string}: observedfeaturesvector.qza" name="oobservedfeaturesvector" />
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92 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector" />
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93 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector" />
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94 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix" />
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95 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix" />
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96 <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults" />
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97 <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults" />
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98 <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.html" name="ojaccardemperor" />
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99 <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.html" name="obraycurtisemperor" />
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100
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101 </outputs>
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102
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103 <help><![CDATA[
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104 Core diversity metrics (non-phylogenetic)
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105 ###############################################################
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106
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107 Applies a collection of diversity metrics (non-phylogenetic) to a feature
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108 table.
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109
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110 Parameters
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111 ----------
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112 table : FeatureTable[Frequency]
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113 The feature table containing the samples over which diversity metrics
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114 should be computed.
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115 sampling_depth : Int % Range(1, None)
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116 The total frequency that each sample should be rarefied to prior to
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117 computing diversity metrics.
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118 metadata : Metadata
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119 The sample metadata to use in the emperor plots.
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120 with_replacement : Bool, optional
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121 Rarefy with replacement by sampling from the multinomial distribution
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122 instead of rarefying without replacement.
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123 n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
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124 [beta methods only] - The number of concurrent jobs to use in
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125 performing this calculation. May not exceed the number of available
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126 physical cores. If n_jobs = 'auto', one job will be launched for each
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127 identified CPU core on the host.
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128
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129 Returns
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130 -------
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131 rarefied_table : FeatureTable[Frequency]
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132 The resulting rarefied feature table.
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133 observed_features_vector : SampleData[AlphaDiversity]
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134 Vector of Observed Features values by sample.
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135 shannon_vector : SampleData[AlphaDiversity]
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136 Vector of Shannon diversity values by sample.
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137 evenness_vector : SampleData[AlphaDiversity]
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138 Vector of Pielou's evenness values by sample.
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139 jaccard_distance_matrix : DistanceMatrix
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140 Matrix of Jaccard distances between pairs of samples.
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141 bray_curtis_distance_matrix : DistanceMatrix
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142 Matrix of Bray-Curtis distances between pairs of samples.
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143 jaccard_pcoa_results : PCoAResults
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144 PCoA matrix computed from Jaccard distances between samples.
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145 bray_curtis_pcoa_results : PCoAResults
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146 PCoA matrix computed from Bray-Curtis distances between samples.
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147 jaccard_emperor : Visualization
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148 Emperor plot of the PCoA matrix computed from Jaccard.
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149 bray_curtis_emperor : Visualization
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150 Emperor plot of the PCoA matrix computed from Bray-Curtis.
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151 ]]></help>
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152 <macros>
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153 <import>qiime_citation.xml</import>
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154 </macros>
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155 <expand macro="qiime_citation"/>
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156 </tool> |
