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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_beta-correlation" name="qiime diversity beta-correlation" version="2019.4">
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3 <description> - Beta diversity correlation</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 beta-correlation
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9
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10 --i-distance-matrix=$idistancematrix
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11 --m-metadata-column="$mmetadatacolumn"
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12
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13 #if str($pmethod) != 'None':
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14 --p-method=$pmethod
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15 #end if
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16
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17 #if $ppermutations:
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18 --p-permutations=$ppermutations
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19 #end if
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20
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21 #if $pintersectids:
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22 --p-intersect-ids
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23 #end if
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24
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25 #if str($plabel1):
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26 --p-label1="$plabel1"
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27 #end if
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28
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29 #if str($plabel2):
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30 --p-label2="$plabel2"
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31 #end if
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32
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33 #if $input_files_mmetadatafile:
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34 #def list_dict_to_string(list_dict):
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35 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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36 #for d in list_dict[1:]:
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37 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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38 #end for
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39 #return $file_list
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40 #end def
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41 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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42 #end if
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43
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44 --o-metadata-distance-matrix=ometadatadistancematrix
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45 --o-mantel-scatter-visualization=omantelscattervisualization
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46 ;
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47 cp ometadatadistancematrix.qza $ometadatadistancematrix;
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48 qiime tools export --input-path omantelscattervisualization.qzv --output-path out && mkdir -p '$omantelscattervisualization.files_path'
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49 && cp -r out/* '$omantelscattervisualization.files_path'
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50 && mv '$omantelscattervisualization.files_path/index.html' '$omantelscattervisualization'
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51 ]]></command>
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52 <inputs>
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53 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
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54 <param label="--m-metadata-column: COLUMN MetadataColumn[Numeric] Numeric metadata column from which to compute pairwise Euclidean distances [required]" name="mmetadatacolumn" optional="False" type="text"/>
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55 <param label="--p-method: " name="pmethod" optional="True" type="select">
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56 <option selected="True" value="None">Selection is Optional</option>
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57 <option value="spearman">spearman</option>
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58 <option value="pearson">pearson</option>
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59 </param>
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60 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
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61 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/>
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62 <param label="--p-label1: TEXT Label for `distance-matrix` in the output visualization. [default: 'Metadata']" name="plabel1" optional="True" type="text" value="'Metadata'"/>
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63 <param label="--p-label2: TEXT Label for `metadata-distance-matrix` in the output visualization. [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="'Distance Matrix'"/>
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64 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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65 <param label="--m-metadata-file" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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66 </repeat>
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67 </inputs>
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68 <outputs>
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69 <data format="qza" label="${tool.name} on ${on_string}: metadatadistancematrix.qza" name="ometadatadistancematrix"/>
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70 <data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.qzv" name="omantelscattervisualization"/>
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71 </outputs>
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72 <help><![CDATA[
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73 Beta diversity correlation
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74 ##########################
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75
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76 Create a distance matrix from a numeric metadata column and apply a two-
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77 sided Mantel test to identify correlation between two distance matrices.
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78 Actions used internally: `distance-matrix` from q2-metadata and `mantel`
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79 from q2-diversity.
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80
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81 Parameters
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82 ----------
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83 metadata : MetadataColumn[Numeric]
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84 Numeric metadata column from which to compute pairwise Euclidean
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85 distances
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86 distance_matrix : DistanceMatrix
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87 Matrix of distances between pairs of samples.
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88 method : Str % Choices('spearman', 'pearson'), optional
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89 The correlation test to be applied in the Mantel test.
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90 permutations : Int % Range(0, None), optional
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91 The number of permutations to be run when computing p-values. Supplying
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92 a value of zero will disable permutation testing and p-values will not
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93 be calculated (this results in *much* quicker execution time if
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94 p-values are not desired).
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95 intersect_ids : Bool, optional
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96 If supplied, IDs that are not found in both distance matrices will be
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97 discarded before applying the Mantel test. Default behavior is to error
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98 on any mismatched IDs.
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99 label1 : Str, optional
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100 Label for `distance_matrix` in the output visualization.
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101 label2 : Str, optional
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102 Label for `metadata_distance_matrix` in the output visualization.
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103
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104 Returns
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105 -------
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106 metadata_distance_matrix : DistanceMatrix
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107 The Distance Matrix produced from the metadata column and used in the
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108 mantel test
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109 mantel_scatter_visualization : Visualization
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110 Scatter plot rendering of the manteltest results
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111 ]]></help>
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112 <macros>
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113 <import>qiime_citation.xml</import>
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114 </macros>
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115 <expand macro="qiime_citation"/>
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116 </tool>
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