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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic"
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3 version="2020.8">
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4 <description>Core diversity metrics (phylogenetic and 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-phylogenetic
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10
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11 --i-table=$itable
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12
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13 --i-phylogeny=$iphylogeny
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14
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15 --p-sampling-depth=$psamplingdepth
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16 # if $input_files_mmetadatafile:
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17 # def list_dict_to_string(list_dict):
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18 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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19 # for d in list_dict[1:]:
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20 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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21 # end for
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22 # return $file_list
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23 # end def
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24 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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25 # end if
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26
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27 #if str($pnjobsorthreads) != 'None':
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28 --p-n-jobs-or-threads=$pnjobsorthreads
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29 #end if
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30
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31 --o-rarefied-table=orarefiedtable
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32
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33 --o-faith-pd-vector=ofaithpdvector
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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-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix
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42
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43 --o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix
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44
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45 --o-jaccard-distance-matrix=ojaccarddistancematrix
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46
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47 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
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48
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49 --o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults
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50
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51 --o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults
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52
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53 --o-jaccard-pcoa-results=ojaccardpcoaresults
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54
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55 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
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56
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57 --o-unweighted-unifrac-emperor=ounweightedunifracemperor
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58
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59 --o-weighted-unifrac-emperor=oweightedunifracemperor
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60
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61 --o-jaccard-emperor=ojaccardemperor
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62
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63 --o-bray-curtis-emperor=obraycurtisemperor
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64
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65 #if str($examples) != 'None':
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66 --examples=$examples
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67 #end if
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68
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69 ;
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70 cp obraycurtispcoaresults.qza $obraycurtispcoaresults
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71
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72 ;
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73 qiime tools export ounweightedunifracemperor.qzv --output-path out
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74 && mkdir -p '$ounweightedunifracemperor.files_path'
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75 && cp -r out/* '$ounweightedunifracemperor.files_path'
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76 && mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor'
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77
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78 ;
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79 qiime tools export oweightedunifracemperor.qzv --output-path out
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80 && mkdir -p '$oweightedunifracemperor.files_path'
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81 && cp -r out/* '$oweightedunifracemperor.files_path'
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82 && mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor'
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83
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84 ;
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85 qiime tools export ojaccardemperor.qzv --output-path out
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86 && mkdir -p '$ojaccardemperor.files_path'
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87 && cp -r out/* '$ojaccardemperor.files_path'
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88 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor'
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89
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90 ;
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91 qiime tools export obraycurtisemperor.qzv --output-path out
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92 && mkdir -p '$obraycurtisemperor.files_path'
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93 && cp -r out/* '$obraycurtisemperor.files_path'
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94 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor'
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95
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96 ]]></command>
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97 <inputs>
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98 <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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99 <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]" name="iphylogeny" optional="False" type="data" />
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100 <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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101 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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102 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments The sample metadata to use in the emperor plots. will be merged) [required]" name="additional_input" optional="False" type="data" />
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103 </repeat>
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104 <param label="--p-n-jobs-or-threads: " name="pnjobsorthreads" optional="True" type="select">
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105 <option selected="True" value="None">Selection is Optional</option>
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106 <option value="Int % Range(1">Int % Range(1</option>
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107 <option value="None">None</option>
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108 </param>
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109 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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110
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111 </inputs>
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112
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113 <outputs>
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114 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable" />
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115 <data format="qza" label="${tool.name} on ${on_string}: faithpdvector.qza" name="ofaithpdvector" />
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116 <data format="qza" label="${tool.name} on ${on_string}: observedfeaturesvector.qza" name="oobservedfeaturesvector" />
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117 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector" />
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118 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector" />
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119 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix" />
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120 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix" />
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121 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix" />
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122 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix" />
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123 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults" />
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124 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults" />
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125 <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults" />
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126 <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults" />
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127 <data format="html" label="${tool.name} on ${on_string}: unweightedunifracemperor.html" name="ounweightedunifracemperor" />
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128 <data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.html" name="oweightedunifracemperor" />
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129 <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.html" name="ojaccardemperor" />
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130 <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.html" name="obraycurtisemperor" />
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131
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132 </outputs>
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133
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134 <help><![CDATA[
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135 Core diversity metrics (phylogenetic and non- phylogenetic)
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136 ###############################################################
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137
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138 Applies a collection of diversity metrics (both phylogenetic and non-
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139 phylogenetic) to a feature table.
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140
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141 Parameters
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142 ----------
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143 table : FeatureTable[Frequency]
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144 The feature table containing the samples over which diversity metrics
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145 should be computed.
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146 phylogeny : Phylogeny[Rooted]
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147 Phylogenetic tree containing tip identifiers that correspond to the
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148 feature identifiers in the table. This tree can contain tip ids that
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149 are not present in the table, but all feature ids in the table must be
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150 present in this tree.
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151 sampling_depth : Int % Range(1, None)
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152 The total frequency that each sample should be rarefied to prior to
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153 computing diversity metrics.
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154 metadata : Metadata
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155 The sample metadata to use in the emperor plots.
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156 n_jobs_or_threads : Int % Range(1, None) | Str % Choices('auto'), optional
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157 [beta/beta-phylogenetic methods only] - The number of concurrent jobs
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158 or CPU threads to use in performing this calculation. Individual
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159 methods will create jobs/threads as implemented in q2-diversity-lib
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160 dependencies. May not exceed the number of available physical cores. If
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161 n_jobs_or_threads = 'auto', one thread/job will be created for each
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162 identified CPU core on the host.
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163
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164 Returns
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165 -------
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166 rarefied_table : FeatureTable[Frequency]
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167 The resulting rarefied feature table.
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168 faith_pd_vector : SampleData[AlphaDiversity]
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169 Vector of Faith PD values by sample.
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170 observed_features_vector : SampleData[AlphaDiversity]
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171 Vector of Observed Features values by sample.
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172 shannon_vector : SampleData[AlphaDiversity]
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173 Vector of Shannon diversity values by sample.
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174 evenness_vector : SampleData[AlphaDiversity]
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175 Vector of Pielou's evenness values by sample.
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176 unweighted_unifrac_distance_matrix : DistanceMatrix
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177 Matrix of unweighted UniFrac distances between pairs of samples.
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178 weighted_unifrac_distance_matrix : DistanceMatrix
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179 Matrix of weighted UniFrac distances between pairs of samples.
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180 jaccard_distance_matrix : DistanceMatrix
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181 Matrix of Jaccard distances between pairs of samples.
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182 bray_curtis_distance_matrix : DistanceMatrix
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183 Matrix of Bray-Curtis distances between pairs of samples.
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184 unweighted_unifrac_pcoa_results : PCoAResults
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185 PCoA matrix computed from unweighted UniFrac distances between samples.
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186 weighted_unifrac_pcoa_results : PCoAResults
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187 PCoA matrix computed from weighted UniFrac distances between samples.
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188 jaccard_pcoa_results : PCoAResults
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189 PCoA matrix computed from Jaccard distances between samples.
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190 bray_curtis_pcoa_results : PCoAResults
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191 PCoA matrix computed from Bray-Curtis distances between samples.
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192 unweighted_unifrac_emperor : Visualization
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193 Emperor plot of the PCoA matrix computed from unweighted UniFrac.
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194 weighted_unifrac_emperor : Visualization
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195 Emperor plot of the PCoA matrix computed from weighted UniFrac.
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196 jaccard_emperor : Visualization
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197 Emperor plot of the PCoA matrix computed from Jaccard.
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198 bray_curtis_emperor : Visualization
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199 Emperor plot of the PCoA matrix computed from Bray-Curtis.
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200 ]]></help>
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201 <macros>
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202 <import>qiime_citation.xml</import>
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203 </macros>
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204 <expand macro="qiime_citation"/>
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205 </tool> |
