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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" version="2019.4">
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3 <description> - Core diversity metrics (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
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9
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10 --i-table=$itable
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4
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11
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12 #if str($psamplingdepth):
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13 --p-sampling-depth="$psamplingdepth"
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14 #end if
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2
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15
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16 #set $pnjobs = '${GALAXY_SLOTS:-4}'
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17 #if str($pnjobs):
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18 --p-n-jobs="$pnjobs"
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19 #end if
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20
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4
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21 #if $input_files_mmetadatafile:
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2
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22 #def list_dict_to_string(list_dict):
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23 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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24 #for d in list_dict[1:]:
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4
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25 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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2
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26 #end for
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27 #return $file_list
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28 #end def
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29 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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4
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30 #end if
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2
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31
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32 --o-rarefied-table=orarefiedtable
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33 --o-observed-otus-vector=oobservedotusvector
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34 --o-shannon-vector=oshannonvector
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35 --o-evenness-vector=oevennessvector
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36 --o-jaccard-distance-matrix=ojaccarddistancematrix
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37 --o-bray-curtis-distance-matrix=obraycurtisdistancematrix
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38 --o-jaccard-pcoa-results=ojaccardpcoaresults
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39 --o-bray-curtis-pcoa-results=obraycurtispcoaresults
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40 --o-jaccard-emperor=ojaccardemperor
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41 --o-bray-curtis-emperor=obraycurtisemperor
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42 ;
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43 cp orarefiedtable.qza $orarefiedtable;
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44 cp oobservedotusvector.qza $oobservedotusvector;
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45 cp oshannonvector.qza $oshannonvector;
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46 cp oevennessvector.qza $oevennessvector;
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47 cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
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48 cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
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49 cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
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50 cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
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51 qiime tools export --input-path ojaccardemperor.qzv --output-path out && mkdir -p '$ojaccardemperor.files_path'
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52 && cp -r out/* '$ojaccardemperor.files_path'
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53 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
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54 qiime tools export --input-path obraycurtisemperor.qzv --output-path out && mkdir -p '$obraycurtisemperor.files_path'
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55 && cp -r out/* '$obraycurtisemperor.files_path'
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56 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
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57 ]]></command>
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58 <inputs>
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59 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data"/>
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60 <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>
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61
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4
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62 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
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2
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63 <param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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64 </repeat>
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65
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66 </inputs>
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67 <outputs>
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68 <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/>
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69 <data format="qza" label="${tool.name} on ${on_string}: observedotusvector.qza" name="oobservedotusvector"/>
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70 <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector"/>
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71 <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector"/>
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72 <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix"/>
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73 <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix"/>
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74 <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults"/>
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75 <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults"/>
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76 <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.qzv" name="ojaccardemperor"/>
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77 <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.qzv" name="obraycurtisemperor"/>
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78 </outputs>
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79 <help><![CDATA[
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80 Core diversity metrics (non-phylogenetic)
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81 #########################################
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82
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83 Applies a collection of diversity metrics (non-phylogenetic) to a feature
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84 table.
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85
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86 Parameters
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87 ----------
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88 table : FeatureTable[Frequency]
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89 The feature table containing the samples over which diversity metrics
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90 should be computed.
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91 sampling_depth : Int % Range(1, None)
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92 The total frequency that each sample should be rarefied to prior to
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93 computing diversity metrics.
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94 metadata : Metadata
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95 The sample metadata to use in the emperor plots.
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96
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97 Returns
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98 -------
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99 rarefied_table : FeatureTable[Frequency]
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100 The resulting rarefied feature table.
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101 observed_otus_vector : SampleData[AlphaDiversity]
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102 Vector of Observed OTUs values by sample.
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103 shannon_vector : SampleData[AlphaDiversity]
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104 Vector of Shannon diversity values by sample.
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105 evenness_vector : SampleData[AlphaDiversity]
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106 Vector of Pielou's evenness values by sample.
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107 jaccard_distance_matrix : DistanceMatrix
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108 Matrix of Jaccard distances between pairs of samples.
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109 bray_curtis_distance_matrix : DistanceMatrix
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110 Matrix of Bray-Curtis distances between pairs of samples.
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111 jaccard_pcoa_results : PCoAResults
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112 PCoA matrix computed from Jaccard distances between samples.
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113 bray_curtis_pcoa_results : PCoAResults
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114 PCoA matrix computed from Bray-Curtis distances between samples.
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115 jaccard_emperor : Visualization
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116 Emperor plot of the PCoA matrix computed from Jaccard.
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117 bray_curtis_emperor : Visualization
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118 Emperor plot of the PCoA matrix computed from Bray-Curtis.
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119 ]]></help>
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120 <macros>
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121 <import>qiime_citation.xml</import>
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122 </macros>
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123 <expand macro="qiime_citation"/>
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124 </tool>
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