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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=$idistancematrix
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4
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11
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12
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13
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14 #if '__sq__' in str($mmetadatacolumn):
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15 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
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16 #set $mmetadatacolumn = $mmetadatacolumn_temp
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17 #end if
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18
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19 --m-metadata-column="$mmetadatacolumn"
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20
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21
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22
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23 #if str($pmethod) != 'None':
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24 --p-method=$pmethod
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25 #end if
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26
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27 #if $ppermutations:
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28 --p-permutations=$ppermutations
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29 #end if
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30
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31 #if $pintersectids:
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32 --p-intersect-ids
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33 #end if
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34
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35
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36
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37
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38 #if '__sq__' in str($plabel1):
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39 #set $plabel1_temp = $plabel1.replace('__sq__', "'")
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40 #set $plabel1 = $plabel1_temp
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41 #end if
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42
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43 #if str($plabel1):
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44 --p-label1="$plabel1"
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45 #end if
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46
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4
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47
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48
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49 #if '__sq__' in str($plabel2):
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50 #set $plabel2_temp = $plabel2.replace('__sq__', "'")
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51 #set $plabel2 = $plabel2_temp
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52 #end if
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53
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54 #if str($plabel2):
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55 --p-label2="$plabel2"
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56 #end if
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57
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58
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59
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60 #if $input_files_mmetadatafile:
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61 #def list_dict_to_string(list_dict):
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62 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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63 #for d in list_dict[1:]:
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64 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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65 #end for
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66 #return $file_list
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67 #end def
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68 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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69 #end if
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70
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71 --o-metadata-distance-matrix=ometadatadistancematrix
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72 --o-mantel-scatter-visualization=omantelscattervisualization
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73 ;
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74 cp ometadatadistancematrix.qza $ometadatadistancematrix;
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75 qiime tools export --input-path omantelscattervisualization.qzv --output-path out && mkdir -p '$omantelscattervisualization.files_path'
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76 && cp -r out/* '$omantelscattervisualization.files_path'
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77 && mv '$omantelscattervisualization.files_path/index.html' '$omantelscattervisualization'
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78 ]]></command>
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79 <inputs>
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80 <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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81 <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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82 <param label="--p-method: " name="pmethod" optional="True" type="select">
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83 <option selected="True" value="None">Selection is Optional</option>
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84 <option value="spearman">spearman</option>
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85 <option value="pearson">pearson</option>
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86 </param>
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87 <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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88 <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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89 <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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90 <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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91 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
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92 <param label="--m-metadata-file" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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93 </repeat>
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94 </inputs>
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95 <outputs>
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96 <data format="qza" label="${tool.name} on ${on_string}: metadatadistancematrix.qza" name="ometadatadistancematrix"/>
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97 <data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.qzv" name="omantelscattervisualization"/>
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98 </outputs>
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99 <help><![CDATA[
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100 Beta diversity correlation
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101 ##########################
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102
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103 Create a distance matrix from a numeric metadata column and apply a two-
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104 sided Mantel test to identify correlation between two distance matrices.
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105 Actions used internally: `distance-matrix` from q2-metadata and `mantel`
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106 from q2-diversity.
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107
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108 Parameters
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109 ----------
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110 metadata : MetadataColumn[Numeric]
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111 Numeric metadata column from which to compute pairwise Euclidean
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112 distances
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113 distance_matrix : DistanceMatrix
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114 Matrix of distances between pairs of samples.
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115 method : Str % Choices('spearman', 'pearson'), optional
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116 The correlation test to be applied in the Mantel test.
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117 permutations : Int % Range(0, None), optional
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118 The number of permutations to be run when computing p-values. Supplying
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119 a value of zero will disable permutation testing and p-values will not
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120 be calculated (this results in *much* quicker execution time if
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121 p-values are not desired).
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122 intersect_ids : Bool, optional
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123 If supplied, IDs that are not found in both distance matrices will be
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124 discarded before applying the Mantel test. Default behavior is to error
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125 on any mismatched IDs.
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126 label1 : Str, optional
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127 Label for `distance_matrix` in the output visualization.
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128 label2 : Str, optional
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129 Label for `metadata_distance_matrix` in the output visualization.
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130
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131 Returns
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132 -------
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133 metadata_distance_matrix : DistanceMatrix
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134 The Distance Matrix produced from the metadata column and used in the
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135 mantel test
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136 mantel_scatter_visualization : Visualization
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137 Scatter plot rendering of the manteltest results
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138 ]]></help>
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139 <macros>
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140 <import>qiime_citation.xml</import>
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141 </macros>
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142 <expand macro="qiime_citation"/>
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143 </tool>
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