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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"
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3 version="2020.8">
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4 <description>Beta diversity correlation</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime diversity beta-correlation
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10
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11 --i-distance-matrix=$idistancematrix
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12 # if $input_files_mmetadatafile:
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13 # def list_dict_to_string(list_dict):
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14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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15 # for d in list_dict[1:]:
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16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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17 # end for
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18 # return $file_list
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19 # end def
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20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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21 # end if
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22
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23 #if '__ob__' in str($mmetadatacolumn):
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24 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
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25 #set $mmetadatacolumn = $mmetadatacolumn_temp
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26 #end if
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27 #if '__cb__' in str($mmetadatacolumn):
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28 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
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29 #set $mmetadatacolumn = $mmetadatacolumn_temp
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30 #end if
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31 #if 'X' in str($mmetadatacolumn):
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32 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
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33 #set $mmetadatacolumn = $mmetadatacolumn_temp
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34 #end if
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35 #if '__sq__' in str($mmetadatacolumn):
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36 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
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37 #set $mmetadatacolumn = $mmetadatacolumn_temp
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38 #end if
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39 #if '__db__' in str($mmetadatacolumn):
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40 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
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41 #set $mmetadatacolumn = $mmetadatacolumn_temp
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42 #end if
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43
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44 --m-metadata-column=$mmetadatacolumn
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45
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46
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47 #if str($pmethod) != 'None':
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48 --p-method=$pmethod
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49 #end if
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50
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51 --p-permutations=$ppermutations
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52
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53 #if $pintersectids:
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54 --p-intersect-ids
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55 #end if
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56
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57 #if str($plabel1):
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58 --p-label1=$plabel1
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59 #end if
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60 #if str($plabel2):
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61 --p-label2=$plabel2
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62 #end if# if $input_files_ometadatadistancematrix:
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63 # def list_dict_to_string(list_dict):
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64 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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65 # for d in list_dict[1:]:
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66 # set $file_list = $file_list + ' --o-metadata-distance-matrix=' + d['additional_input'].__getattr__('file_name')
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67 # end for
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68 # return $file_list
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69 # end def
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70 --o-metadata-distance-matrix=$list_dict_to_string($input_files_ometadatadistancematrix)
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71 # end if
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72
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73 --o-mantel-scatter-visualization=omantelscattervisualization
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74
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75 #if str($examples) != 'None':
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76 --examples=$examples
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77 #end if
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78
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79 ;
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80 cp odistancematrix.qza $odistancematrix
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81
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82 ;
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83 qiime tools export omantelscattervisualization.qzv --output-path out
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84 && mkdir -p '$omantelscattervisualization.files_path'
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85 && cp -r out/* '$omantelscattervisualization.files_path'
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86 && mv '$omantelscattervisualization.files_path/index.html' '$omantelscattervisualization'
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87
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88 ]]></command>
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89 <inputs>
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90 <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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91 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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92 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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93 </repeat>
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94 <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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95 <param label="--p-method: " name="pmethod" optional="True" type="select">
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96 <option selected="True" value="None">Selection is Optional</option>
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97 <option value="spearman">spearman</option>
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98 <option value="pearson">pearson</option>
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99 </param>
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100 <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]" min="0" name="ppermutations" optional="True" type="integer" value="999" />
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101 <param label="--p-intersect-ids: --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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102 <param label="--p-label1: TEXT Label for `distance-matrix` in the output visualization. [default: \'Metadata\']" name="plabel1" optional="False" type="text" value="\'Metadata\'" />
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103 <param label="--p-label2: TEXT Label for `metadata-distance-matrix` in the output visualization. [default: \'Distance Matrix\']" name="plabel2" optional="False" type="text" value="\'Distance Matrix\'" />
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104 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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105
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106 </inputs>
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107
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108 <outputs>
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109 <repeat name="input_files_ometadatadistancematrix" optional="False" title="--o-metadata-distance-matrix">
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110 <param format="tabular,qza,no_unzip.zip" label="--o-metadata-distance-matrix: ARTIFACT DistanceMatrix The Distance Matrix produced from the metadata column and used in the mantel test [required]" name="additional_input" optional="False" type="data" />
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111 </repeat>
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112 <data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.html" name="omantelscattervisualization" />
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113
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114 </outputs>
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115
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116 <help><![CDATA[
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117 Beta diversity correlation
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118 ###############################################################
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119
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120 Create a distance matrix from a numeric metadata column and apply a two-
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121 sided Mantel test to identify correlation between two distance matrices.
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122 Actions used internally: `distance-matrix` from q2-metadata and `mantel`
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123 from q2-diversity.
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124
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125 Parameters
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126 ----------
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127 metadata : MetadataColumn[Numeric]
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128 Numeric metadata column from which to compute pairwise Euclidean
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129 distances
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130 distance_matrix : DistanceMatrix
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131 Matrix of distances between pairs of samples.
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132 method : Str % Choices('spearman', 'pearson'), optional
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133 The correlation test to be applied in the Mantel test.
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134 permutations : Int % Range(0, None), optional
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135 The number of permutations to be run when computing p-values. Supplying
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136 a value of zero will disable permutation testing and p-values will not
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137 be calculated (this results in *much* quicker execution time if
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138 p-values are not desired).
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139 intersect_ids : Bool, optional
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140 If supplied, IDs that are not found in both distance matrices will be
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141 discarded before applying the Mantel test. Default behavior is to error
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142 on any mismatched IDs.
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143 label1 : Str, optional
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144 Label for `distance_matrix` in the output visualization.
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145 label2 : Str, optional
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146 Label for `metadata_distance_matrix` in the output visualization.
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147
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148 Returns
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149 -------
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150 metadata_distance_matrix : DistanceMatrix
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151 The Distance Matrix produced from the metadata column and used in the
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152 mantel test
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153 mantel_scatter_visualization : Visualization
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154 Scatter plot rendering of the manteltest results
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155 ]]></help>
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156 <macros>
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157 <import>qiime_citation.xml</import>
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158 </macros>
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159 <expand macro="qiime_citation"/>
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160 </tool> |
