annotate qiime2-2020.8/qiime_sample-classifier_confusion-matrix.xml @ 25:499916460746 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:56:26 +0000
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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"
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3 version="2020.8">
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4 <description>Make a confusion matrix from sample classifier predictions.</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 confusion-matrix
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10
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11 --i-predictions=$ipredictions
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12
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13 #if str($iprobabilities) != 'None':
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14 --i-probabilities=$iprobabilities
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15 #end if
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16
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17 #if str($mtruthfile) != 'None':
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18 --m-truth-file=$mtruthfile
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19 #end if
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20
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21 #if '__ob__' in str($mtruthcolumn):
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22 #set $mtruthcolumn_temp = $mtruthcolumn.replace('__ob__', '[')
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23 #set $mtruthcolumn = $mtruthcolumn_temp
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24 #end if
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25 #if '__cb__' in str($mtruthcolumn):
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26 #set $mtruthcolumn_temp = $mtruthcolumn.replace('__cb__', ']')
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27 #set $mtruthcolumn = $mtruthcolumn_temp
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28 #end if
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29 #if 'X' in str($mtruthcolumn):
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30 #set $mtruthcolumn_temp = $mtruthcolumn.replace('X', '\\')
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31 #set $mtruthcolumn = $mtruthcolumn_temp
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32 #end if
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33 #if '__sq__' in str($mtruthcolumn):
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34 #set $mtruthcolumn_temp = $mtruthcolumn.replace('__sq__', "'")
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35 #set $mtruthcolumn = $mtruthcolumn_temp
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36 #end if
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37 #if '__db__' in str($mtruthcolumn):
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38 #set $mtruthcolumn_temp = $mtruthcolumn.replace('__db__', '"')
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39 #set $mtruthcolumn = $mtruthcolumn_temp
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40 #end if
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41
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42 --m-truth-column=$mtruthcolumn
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43
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44
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45 #if str($pmissingsamples) != 'None':
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46 --p-missing-samples=$pmissingsamples
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47 #end if
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48
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49 #if str($pvmin) != 'None':
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50 --p-vmin=$pvmin
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51 #end if
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52
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53 #if str($pvmax) != 'None':
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54 --p-vmax=$pvmax
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55 #end if
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56
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57 #if str($ppalette) != 'None':
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58 --p-palette=$ppalette
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59 #end if
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60
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61 --o-visualization=ovisualization
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62
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63 #if str($examples) != 'None':
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64 --examples=$examples
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65 #end if
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66
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67 ;
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68 cp oprobabilities.qza $oprobabilities
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69
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70 ;
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71 qiime tools export ovisualization.qzv --output-path out
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72 && mkdir -p '$ovisualization.files_path'
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73 && cp -r out/* '$ovisualization.files_path'
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74 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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75
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76 ]]></command>
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77 <inputs>
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78 <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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79 <param format="qza,no_unzip.zip" label="--i-probabilities: ARTIFACT SampleData[Probabilities] Predicted class probabilities for each input sample. [optional]" name="iprobabilities" optional="False" type="data" />
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80 <param label="--m-truth-file: METADATA" name="mtruthfile" optional="False" type="data" />
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81 <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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82 <param label="--p-missing-samples: " name="pmissingsamples" 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="error">error</option>
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85 <option value="ignore">ignore</option>
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86 </param>
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87 <param label="--p-vmin: " name="pvmin" optional="True" type="select">
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88 <option selected="True" value="None">Selection is Optional</option>
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89 <option value="auto">auto</option>
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90 </param>
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91 <param label="--p-vmax: " name="pvmax" optional="True" type="select">
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92 <option selected="True" value="None">Selection is Optional</option>
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93 <option value="auto">auto</option>
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94 </param>
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95 <param label="--p-palette: " name="ppalette" 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="YellowOrangeBrown">YellowOrangeBrown</option>
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98 <option value="YellowOrangeRed">YellowOrangeRed</option>
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99 <option value="OrangeRed">OrangeRed</option>
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100 <option value="PurpleRed">PurpleRed</option>
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101 <option value="RedPurple">RedPurple</option>
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102 <option value="BluePurple">BluePurple</option>
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103 <option value="GreenBlue">GreenBlue</option>
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104 <option value="PurpleBlue">PurpleBlue</option>
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105 <option value="YellowGreen">YellowGreen</option>
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106 <option value="summer">summer</option>
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107 <option value="copper">copper</option>
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108 <option value="viridis">viridis</option>
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109 <option value="cividis">cividis</option>
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110 <option value="plasma">plasma</option>
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111 <option value="inferno">inferno</option>
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112 <option value="magma">magma</option>
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113 <option value="sirocco">sirocco</option>
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114 <option value="drifting">drifting</option>
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115 <option value="melancholy">melancholy</option>
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116 <option value="enigma">enigma</option>
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117 <option value="eros">eros</option>
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118 <option value="spectre">spectre</option>
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119 <option value="ambition">ambition</option>
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120 <option value="mysteriousstains">mysteriousstains</option>
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121 <option value="daydream">daydream</option>
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122 <option value="solano">solano</option>
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123 <option value="navarro">navarro</option>
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124 <option value="dandelions">dandelions</option>
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125 <option value="deepblue">deepblue</option>
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126 <option value="verve">verve</option>
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127 <option value="greyscale">greyscale</option>
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128 </param>
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129 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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130
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131 </inputs>
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132
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133 <outputs>
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134 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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135
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136 </outputs>
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137
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138 <help><![CDATA[
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139 Make a confusion matrix from sample classifier predictions.
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140 ###############################################################
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141
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142 Make a confusion matrix and calculate accuracy of predicted vs. true values
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143 for a set of samples classified using a sample classifier. If per-sample
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144 class probabilities are provided, will also generate Receiver Operating
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145 Characteristic curves and calculate area under the curve for each class.
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146
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147 Parameters
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148 ----------
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149 predictions : SampleData[ClassifierPredictions]
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150 Predicted values to plot on x axis. Should be predictions of
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151 categorical data produced by a sample classifier.
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152 truth : MetadataColumn[Categorical]
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153 Metadata column (true values) to plot on y axis.
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154 probabilities : SampleData[Probabilities], optional
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155 Predicted class probabilities for each input sample.
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156 missing_samples : Str % Choices('error', 'ignore'), optional
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157 How to handle missing samples in metadata. "error" will fail if missing
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158 samples are detected. "ignore" will cause the feature table and
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159 metadata to be filtered, so that only samples found in both files are
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160 retained.
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161 vmin : Float | Str % Choices('auto'), optional
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162 The minimum value to use for anchoring the colormap. If "auto", vmin is
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163 set to the minimum value in the data.
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164 vmax : Float | Str % Choices('auto'), optional
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165 The maximum value to use for anchoring the colormap. If "auto", vmax is
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166 set to the maximum value in the data.
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167 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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168 The color palette to use for plotting.
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169
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170 Returns
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171 -------
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172 visualization : Visualization
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173 ]]></help>
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174 <macros>
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175 <import>qiime_citation.xml</import>
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176 </macros>
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177 <expand macro="qiime_citation"/>
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178 </tool>