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