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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" version="2019.4">
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3 <description> - Run k-nearest-neighbors on a labeled distance matrix.</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 sample-classifier classify-samples-from-dist
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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 $pk:
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14 --p-k=$pk
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15 #end if
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16
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17 #if str($ppalette) != 'None':
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18 --p-palette=$ppalette
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19 #end if
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20
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21
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22 #if $input_files_mmetadatafile:
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23 #def list_dict_to_string(list_dict):
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24 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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25 #for d in list_dict[1:]:
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26 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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27 #end for
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28 #return $file_list
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29 #end def
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30 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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31 #end if
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32
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33
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34 --o-predictions=opredictions
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35 --o-accuracy-results=oaccuracyresults
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36 ;
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37 cp opredictions.qza $opredictions;
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38 qiime tools export --input-path oaccuracyresults.qzv --output-path out && mkdir -p '$oaccuracyresults.files_path'
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39 && cp -r out/* '$oaccuracyresults.files_path'
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40 && mv '$oaccuracyresults.files_path/index.html' '$oaccuracyresults'
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41 ]]></command>
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42 <inputs>
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43 <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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44 <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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45 <param label="--p-k: INTEGER Number of nearest neighbors [default: 1]" name="pk" optional="True" type="integer" value="1"/>
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46 <param label="--p-palette: " name="ppalette" optional="True" type="select">
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47 <option selected="True" value="None">Selection is Optional</option>
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48 <option value="YellowOrangeBrown">YellowOrangeBrown</option>
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49 <option value="YellowOrangeRed">YellowOrangeRed</option>
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50 <option value="OrangeRed">OrangeRed</option>
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51 <option value="PurpleRed">PurpleRed</option>
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52 <option value="RedPurple">RedPurple</option>
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53 <option value="BluePurple">BluePurple</option>
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54 <option value="GreenBlue">GreenBlue</option>
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55 <option value="PurpleBlue">PurpleBlue</option>
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56 <option value="YellowGreen">YellowGreen</option>
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57 <option value="summer">summer</option>
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58 <option value="copper">copper</option>
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59 <option value="viridis">viridis</option>
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60 <option value="plasma">plasma</option>
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61 <option value="inferno">inferno</option>
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62 <option value="magma">magma</option>
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63 <option value="sirocco">sirocco</option>
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64 <option value="drifting">drifting</option>
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65 <option value="melancholy">melancholy</option>
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66 <option value="enigma">enigma</option>
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67 <option value="eros">eros</option>
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68 <option value="spectre">spectre</option>
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69 <option value="ambition">ambition</option>
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70 <option value="mysteriousstains">mysteriousstains</option>
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71 <option value="daydream">daydream</option>
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72 <option value="solano">solano</option>
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73 <option value="navarro">navarro</option>
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74 <option value="dandelions">dandelions</option>
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75 <option value="deepblue">deepblue</option>
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76 <option value="verve">verve</option>
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77 <option value="greyscale">greyscale</option>
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78 </param>
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79
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80 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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81 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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82 </repeat>
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83
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84 </inputs>
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85 <outputs>
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86 <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/>
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87 <data format="html" label="${tool.name} on ${on_string}: accuracyresults.qzv" name="oaccuracyresults"/>
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88 </outputs>
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89 <help><![CDATA[
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90 Run k-nearest-neighbors on a labeled distance matrix.
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91 #####################################################
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92
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93 Run k-nearest-neighbors on a labeled distance matrix. Return cross-
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94 validated (leave one out) predictions and accuracy. k = 1 by default
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95
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96 Parameters
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97 ----------
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98 distance_matrix : DistanceMatrix
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99 a distance matrix
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100 metadata : MetadataColumn[Categorical]
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101 Categorical metadata column to use as prediction target.
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102 k : Int, optional
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103 Number of nearest neighbors
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104 palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional
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105 The color palette to use for plotting.
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106
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107 Returns
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108 -------
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109 predictions : SampleData[ClassifierPredictions]
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110 leave one out predictions for each sample
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111 accuracy_results : Visualization
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112 Accuracy results visualization.
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113 ]]></help>
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114 <macros>
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115 <import>qiime_citation.xml</import>
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116 </macros>
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117 <expand macro="qiime_citation"/>
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118 </tool>
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