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