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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" version="2019.4">
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3 <description> - Core diversity metrics (phylogenetic and non- phylogenetic)</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 core-metrics-phylogenetic
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9
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10 --i-table=$itable
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11 --i-phylogeny=$iphylogeny
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6
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12
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13 #if str($psamplingdepth):
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14 --p-sampling-depth="$psamplingdepth"
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15 #end if
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0
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16
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17 #set $pnjobs = '${GALAXY_SLOTS:-4}'
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18 #if str($pnjobs):
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19 --p-n-jobs="$pnjobs"
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20 #end if
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21
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2
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22
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23 #if $input_files_mmetadatafile:
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0
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24 #def list_dict_to_string(list_dict):
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25 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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26 #for d in list_dict[1:]:
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6
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27 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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28 #end for
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29 #return $file_list
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30 #end def
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2
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31 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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32 #end if
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0
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33
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34
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35
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36 --o-rarefied-table=orarefiedtable
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37 --o-faith-pd-vector=ofaithpdvector
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38 --o-observed-otus-vector=oobservedotusvector
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39 --o-shannon-vector=oshannonvector
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40 --o-evenness-vector=oevennessvector
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41 --o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix
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42 --o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix
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43 --o-jaccard-distance-matrix=ojaccarddistancematrix
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44 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
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45 --o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults
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46 --o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults
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47 --o-jaccard-pcoa-results=ojaccardpcoaresults
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48 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
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49 --o-unweighted-unifrac-emperor=ounweightedunifracemperor
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50 --o-weighted-unifrac-emperor=oweightedunifracemperor
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51 --o-jaccard-emperor=ojaccardemperor
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52 --o-bray-curtis-emperor=obraycurtisemperor
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53 ;
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54 cp orarefiedtable.qza $orarefiedtable;
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55 cp ofaithpdvector.qza $ofaithpdvector;
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56 cp oobservedotusvector.qza $oobservedotusvector;
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57 cp oshannonvector.qza $oshannonvector;
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58 cp oevennessvector.qza $oevennessvector;
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59 cp ounweightedunifracdistancematrix.qza $ounweightedunifracdistancematrix;
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60 cp oweightedunifracdistancematrix.qza $oweightedunifracdistancematrix;
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61 cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
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62 cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
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63 cp ounweightedunifracpcoaresults.qza $ounweightedunifracpcoaresults;
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64 cp oweightedunifracpcoaresults.qza $oweightedunifracpcoaresults;
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65 cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
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66 cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
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67 qiime tools export --input-path ounweightedunifracemperor.qzv --output-path out && mkdir -p '$ounweightedunifracemperor.files_path'
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68 && cp -r out/* '$ounweightedunifracemperor.files_path'
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69 && mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor';
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70 qiime tools export --input-path oweightedunifracemperor.qzv --output-path out && mkdir -p '$oweightedunifracemperor.files_path'
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71 && cp -r out/* '$oweightedunifracemperor.files_path'
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72 && mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor';
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73 qiime tools export --input-path ojaccardemperor.qzv --output-path out && mkdir -p '$ojaccardemperor.files_path'
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74 && cp -r out/* '$ojaccardemperor.files_path'
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75 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
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76 qiime tools export --input-path obraycurtisemperor.qzv --output-path out && mkdir -p '$obraycurtisemperor.files_path'
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77 && cp -r out/* '$obraycurtisemperor.files_path'
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78 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
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79 ]]></command>
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80 <inputs>
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81 <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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82 <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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83 <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" min="1" value="" type="integer"/>
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84
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4
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85 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
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86 <param label="--m-metadata-file: (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" optional="False" type="data" format="tabular,qza,no_unzip.zip" />
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0
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87 </repeat>
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88
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89 </inputs>
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90 <outputs>
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91 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/>
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92 <data format="qza" label="${tool.name} on ${on_string}: faithpdvector.qza" name="ofaithpdvector"/>
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93 <data format="qza" label="${tool.name} on ${on_string}: observedotusvector.qza" name="oobservedotusvector"/>
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94 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector"/>
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95 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector"/>
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96 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix"/>
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97 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix"/>
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98 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix"/>
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99 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix"/>
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100 <data format="qza" label="${tool.name} on ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults"/>
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101 <data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults"/>
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102 <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults"/>
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103 <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults"/>
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104 <data format="html" label="${tool.name} on ${on_string}: unweightedunifracemperor.qzv" name="ounweightedunifracemperor"/>
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105 <data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.qzv" name="oweightedunifracemperor"/>
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106 <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.qzv" name="ojaccardemperor"/>
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107 <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.qzv" name="obraycurtisemperor"/>
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108 </outputs>
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109 <help><![CDATA[
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110 Core diversity metrics (phylogenetic and non-phylogenetic)
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111 ##########################################################
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112
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113 Applies a collection of diversity metrics (both phylogenetic and non-
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114 phylogenetic) to a feature table.
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115
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116 Parameters
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117 ----------
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118 table : FeatureTable[Frequency]
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119 The feature table containing the samples over which diversity metrics
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120 should be computed.
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121 phylogeny : Phylogeny[Rooted]
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122 Phylogenetic tree containing tip identifiers that correspond to the
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123 feature identifiers in the table. This tree can contain tip ids that
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124 are not present in the table, but all feature ids in the table must be
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125 present in this tree.
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126 sampling_depth : Int % Range(1, None)
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127 The total frequency that each sample should be rarefied to prior to
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128 computing diversity metrics.
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129 metadata : Metadata
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130 The sample metadata to use in the emperor plots.
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131
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132 Returns
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133 -------
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134 rarefied_table : FeatureTable[Frequency]
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135 The resulting rarefied feature table.
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136 faith_pd_vector : SampleData[AlphaDiversity]
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137 Vector of Faith PD values by sample.
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138 observed_otus_vector : SampleData[AlphaDiversity]
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139 Vector of Observed OTUs values by sample.
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140 shannon_vector : SampleData[AlphaDiversity]
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141 Vector of Shannon diversity values by sample.
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142 evenness_vector : SampleData[AlphaDiversity]
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143 Vector of Pielou's evenness values by sample.
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144 unweighted_unifrac_distance_matrix : DistanceMatrix
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145 Matrix of unweighted UniFrac distances between pairs of samples.
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146 weighted_unifrac_distance_matrix : DistanceMatrix
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147 Matrix of weighted UniFrac distances between pairs of samples.
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148 jaccard_distance_matrix : DistanceMatrix
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149 Matrix of Jaccard distances between pairs of samples.
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150 bray_curtis_distance_matrix : DistanceMatrix
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151 Matrix of Bray-Curtis distances between pairs of samples.
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152 unweighted_unifrac_pcoa_results : PCoAResults
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153 PCoA matrix computed from unweighted UniFrac distances between samples.
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154 weighted_unifrac_pcoa_results : PCoAResults
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155 PCoA matrix computed from weighted UniFrac distances between samples.
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156 jaccard_pcoa_results : PCoAResults
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157 PCoA matrix computed from Jaccard distances between samples.
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158 bray_curtis_pcoa_results : PCoAResults
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159 PCoA matrix computed from Bray-Curtis distances between samples.
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160 unweighted_unifrac_emperor : Visualization
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161 Emperor plot of the PCoA matrix computed from unweighted UniFrac.
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162 weighted_unifrac_emperor : Visualization
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163 Emperor plot of the PCoA matrix computed from weighted UniFrac.
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164 jaccard_emperor : Visualization
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165 Emperor plot of the PCoA matrix computed from Jaccard.
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166 bray_curtis_emperor : Visualization
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167 Emperor plot of the PCoA matrix computed from Bray-Curtis.
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168 ]]></help>
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169 <macros>
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170 <import>qiime_citation.xml</import>
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171 </macros>
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172 <expand macro="qiime_citation"/>
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173 </tool>
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