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1 <?xml version="1.0" ?>
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2 <tool id="qiime_sample-classifier_confusion-matrix" name="qiime sample-classifier confusion-matrix" version="2019.4">
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3 <description> - Make a confusion matrix from sample classifier predictions.</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 confusion-matrix
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9
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10 --i-predictions=$ipredictions
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11 --m-truth-column="$mtruthcolumn"
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12 --m-truth-file=mtruthfile
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13
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14 #if str($pmissingsamples) != 'None':
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15 --p-missing-samples=$pmissingsamples
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16 #end if
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17
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18 #if str($ppalette) != 'None':
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19 --p-palette=$ppalette
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20 #end if
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21
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22 --o-visualization=ovisualization
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23 ;
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24 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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25 && cp -r out/* '$ovisualization.files_path'
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26 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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27 cp mtruthfile.qza $mtruthfile
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28 ]]></command>
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29 <inputs>
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30 <param format="qza,no_unzip.zip" label="--i-predictions: ARTIFACT SampleData[ClassifierPredictions] Predicted values to plot on x axis. Should be predictions of categorical data produced by a sample classifier. [required]" name="ipredictions" optional="False" type="data"/>
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31 <param label="--m-truth-column: COLUMN MetadataColumn[Categorical] Metadata column (true values) to plot on y axis. [required]" name="mtruthcolumn" optional="False" type="text"/>
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32 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
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33 <option selected="True" value="None">Selection is Optional</option>
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34 <option value="error">error</option>
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35 <option value="ignore">ignore</option>
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36 </param>
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37 <param label="--p-palette: " name="ppalette" optional="True" type="select">
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38 <option selected="True" value="None">Selection is Optional</option>
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39 <option value="YellowOrangeBrown">YellowOrangeBrown</option>
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40 <option value="YellowOrangeRed">YellowOrangeRed</option>
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41 <option value="OrangeRed">OrangeRed</option>
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42 <option value="PurpleRed">PurpleRed</option>
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43 <option value="RedPurple">RedPurple</option>
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44 <option value="BluePurple">BluePurple</option>
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45 <option value="GreenBlue">GreenBlue</option>
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46 <option value="PurpleBlue">PurpleBlue</option>
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47 <option value="YellowGreen">YellowGreen</option>
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48 <option value="summer">summer</option>
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49 <option value="copper">copper</option>
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50 <option value="viridis">viridis</option>
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51 <option value="plasma">plasma</option>
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52 <option value="inferno">inferno</option>
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53 <option value="magma">magma</option>
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54 <option value="sirocco">sirocco</option>
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55 <option value="drifting">drifting</option>
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56 <option value="melancholy">melancholy</option>
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57 <option value="enigma">enigma</option>
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58 <option value="eros">eros</option>
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59 <option value="spectre">spectre</option>
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60 <option value="ambition">ambition</option>
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61 <option value="mysteriousstains">mysteriousstains</option>
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62 <option value="daydream">daydream</option>
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63 <option value="solano">solano</option>
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64 <option value="navarro">navarro</option>
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65 <option value="dandelions">dandelions</option>
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66 <option value="deepblue">deepblue</option>
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67 <option value="verve">verve</option>
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68 <option value="greyscale">greyscale</option>
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69 </param>
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70 </inputs>
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71 <outputs>
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72 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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73 <data format="qza" label="${tool.name} on ${on_string}: truthfile.qza" name="mtruthfile"/>
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74 </outputs>
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75 <help><![CDATA[
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76 Make a confusion matrix from sample classifier predictions.
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77 ###########################################################
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78
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79 Make a confusion matrix and calculate accuracy of predicted vs. true values
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80 for a set of samples classified using a sample classifier.
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81
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82 Parameters
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83 ----------
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84 predictions : SampleData[ClassifierPredictions]
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85 Predicted values to plot on x axis. Should be predictions of
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86 categorical data produced by a sample classifier.
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87 truth : MetadataColumn[Categorical]
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88 Metadata column (true values) to plot on y axis.
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89 missing_samples : Str % Choices('error', 'ignore'), optional
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90 How to handle missing samples in metadata. "error" will fail if missing
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91 samples are detected. "ignore" will cause the feature table and
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92 metadata to be filtered, so that only samples found in both files are
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93 retained.
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94 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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95 The color palette to use for plotting.
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96
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97 Returns
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98 -------
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99 visualization : Visualization
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100 ]]></help>
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101 <macros>
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102 <import>qiime_citation.xml</import>
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103 </macros>
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104 <expand macro="qiime_citation"/>
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105 </tool>
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