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1 <?xml version="1.0" ?>
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2 <tool id="qiime_sample-classifier_classify-samples-from-dist" name="qiime sample-classifier classify-samples-from-dist"
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3 version="2020.8">
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4 <description>Run k-nearest-neighbors on a labeled distance matrix.</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 sample-classifier classify-samples-from-dist
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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 --p-k=$pk
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48
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49 #if str($ppalette) != 'None':
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50 --p-palette=$ppalette
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51 #end if
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52
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53 --o-predictions=opredictions
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54
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55 --o-accuracy-results=oaccuracyresults
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56
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57 #if str($examples) != 'None':
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58 --examples=$examples
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59 #end if
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60
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61 ;
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62 cp opredictions.qza $opredictions
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63
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64 ;
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65 qiime tools export oaccuracyresults.qzv --output-path out
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66 && mkdir -p '$oaccuracyresults.files_path'
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67 && cp -r out/* '$oaccuracyresults.files_path'
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68 && mv '$oaccuracyresults.files_path/index.html' '$oaccuracyresults'
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69
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70 ]]></command>
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71 <inputs>
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72 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix a distance matrix [required]" name="idistancematrix" optional="False" type="data" />
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73 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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74 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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75 </repeat>
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76 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text" />
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77 <param label="--p-k: INTEGER Number of nearest neighbors [default: 1]" name="pk" optional="True" type="integer" value="1" />
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78 <param label="--p-palette: " name="ppalette" optional="True" type="select">
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79 <option selected="True" value="None">Selection is Optional</option>
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80 <option value="YellowOrangeBrown">YellowOrangeBrown</option>
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81 <option value="YellowOrangeRed">YellowOrangeRed</option>
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82 <option value="OrangeRed">OrangeRed</option>
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83 <option value="PurpleRed">PurpleRed</option>
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84 <option value="RedPurple">RedPurple</option>
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85 <option value="BluePurple">BluePurple</option>
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86 <option value="GreenBlue">GreenBlue</option>
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87 <option value="PurpleBlue">PurpleBlue</option>
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88 <option value="YellowGreen">YellowGreen</option>
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89 <option value="summer">summer</option>
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90 <option value="copper">copper</option>
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91 <option value="viridis">viridis</option>
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92 <option value="cividis">cividis</option>
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93 <option value="plasma">plasma</option>
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94 <option value="inferno">inferno</option>
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95 <option value="magma">magma</option>
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96 <option value="sirocco">sirocco</option>
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97 <option value="drifting">drifting</option>
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98 <option value="melancholy">melancholy</option>
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99 <option value="enigma">enigma</option>
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100 <option value="eros">eros</option>
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101 <option value="spectre">spectre</option>
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102 <option value="ambition">ambition</option>
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103 <option value="mysteriousstains">mysteriousstains</option>
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104 <option value="daydream">daydream</option>
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105 <option value="solano">solano</option>
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106 <option value="navarro">navarro</option>
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107 <option value="dandelions">dandelions</option>
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108 <option value="deepblue">deepblue</option>
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109 <option value="verve">verve</option>
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110 <option value="greyscale">greyscale</option>
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111 </param>
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112 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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113
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114 </inputs>
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115
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116 <outputs>
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117 <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions" />
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118 <data format="html" label="${tool.name} on ${on_string}: accuracyresults.html" name="oaccuracyresults" />
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119
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120 </outputs>
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121
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122 <help><![CDATA[
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123 Run k-nearest-neighbors on a labeled distance matrix.
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124 ###############################################################
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125
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126 Run k-nearest-neighbors on a labeled distance matrix. Return cross-
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127 validated (leave one out) predictions and accuracy. k = 1 by default
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128
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129 Parameters
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130 ----------
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131 distance_matrix : DistanceMatrix
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132 a distance matrix
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133 metadata : MetadataColumn[Categorical]
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134 Categorical metadata column to use as prediction target.
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135 k : Int, optional
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136 Number of nearest neighbors
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137 palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'cividis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional
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138 The color palette to use for plotting.
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139
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140 Returns
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141 -------
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142 predictions : SampleData[ClassifierPredictions]
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143 leave one out predictions for each sample
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144 accuracy_results : Visualization
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145 Accuracy results visualization.
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146 ]]></help>
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147 <macros>
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148 <import>qiime_citation.xml</import>
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149 </macros>
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150 <expand macro="qiime_citation"/>
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151 </tool> |
