|
0
|
1 <?xml version="1.0" ?>
|
|
9
|
2 <tool id="qiime_sample-classifier_confusion-matrix" name="qiime sample-classifier confusion-matrix" version="2019.7">
|
|
0
|
3 <description> - Make a confusion matrix from sample classifier predictions.</description>
|
|
|
4 <requirements>
|
|
9
|
5 <requirement type="package" version="2019.7">qiime2</requirement>
|
|
0
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime sample-classifier confusion-matrix
|
|
|
9
|
|
|
10 --i-predictions=$ipredictions
|
|
|
11 --m-truth-column="$mtruthcolumn"
|
|
|
12 --m-truth-file=mtruthfile
|
|
|
13
|
|
|
14 #if str($pmissingsamples) != 'None':
|
|
|
15 --p-missing-samples=$pmissingsamples
|
|
|
16 #end if
|
|
|
17
|
|
|
18 #if str($ppalette) != 'None':
|
|
|
19 --p-palette=$ppalette
|
|
|
20 #end if
|
|
|
21
|
|
|
22 --o-visualization=ovisualization
|
|
|
23 ;
|
|
|
24 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
25 && cp -r out/* '$ovisualization.files_path'
|
|
|
26 && mv '$ovisualization.files_path/index.html' '$ovisualization';
|
|
|
27 cp mtruthfile.qza $mtruthfile
|
|
|
28 ]]></command>
|
|
|
29 <inputs>
|
|
|
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"/>
|
|
|
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"/>
|
|
|
32 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
|
|
|
33 <option selected="True" value="None">Selection is Optional</option>
|
|
|
34 <option value="error">error</option>
|
|
|
35 <option value="ignore">ignore</option>
|
|
|
36 </param>
|
|
|
37 <param label="--p-palette: " name="ppalette" optional="True" type="select">
|
|
|
38 <option selected="True" value="None">Selection is Optional</option>
|
|
|
39 <option value="YellowOrangeBrown">YellowOrangeBrown</option>
|
|
|
40 <option value="YellowOrangeRed">YellowOrangeRed</option>
|
|
|
41 <option value="OrangeRed">OrangeRed</option>
|
|
|
42 <option value="PurpleRed">PurpleRed</option>
|
|
|
43 <option value="RedPurple">RedPurple</option>
|
|
|
44 <option value="BluePurple">BluePurple</option>
|
|
|
45 <option value="GreenBlue">GreenBlue</option>
|
|
|
46 <option value="PurpleBlue">PurpleBlue</option>
|
|
|
47 <option value="YellowGreen">YellowGreen</option>
|
|
|
48 <option value="summer">summer</option>
|
|
|
49 <option value="copper">copper</option>
|
|
|
50 <option value="viridis">viridis</option>
|
|
|
51 <option value="plasma">plasma</option>
|
|
|
52 <option value="inferno">inferno</option>
|
|
|
53 <option value="magma">magma</option>
|
|
|
54 <option value="sirocco">sirocco</option>
|
|
|
55 <option value="drifting">drifting</option>
|
|
|
56 <option value="melancholy">melancholy</option>
|
|
|
57 <option value="enigma">enigma</option>
|
|
|
58 <option value="eros">eros</option>
|
|
|
59 <option value="spectre">spectre</option>
|
|
|
60 <option value="ambition">ambition</option>
|
|
|
61 <option value="mysteriousstains">mysteriousstains</option>
|
|
|
62 <option value="daydream">daydream</option>
|
|
|
63 <option value="solano">solano</option>
|
|
|
64 <option value="navarro">navarro</option>
|
|
|
65 <option value="dandelions">dandelions</option>
|
|
|
66 <option value="deepblue">deepblue</option>
|
|
|
67 <option value="verve">verve</option>
|
|
|
68 <option value="greyscale">greyscale</option>
|
|
|
69 </param>
|
|
|
70 </inputs>
|
|
|
71 <outputs>
|
|
|
72 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
73 <data format="qza" label="${tool.name} on ${on_string}: truthfile.qza" name="mtruthfile"/>
|
|
|
74 </outputs>
|
|
|
75 <help><![CDATA[
|
|
|
76 Make a confusion matrix from sample classifier predictions.
|
|
|
77 ###########################################################
|
|
|
78
|
|
|
79 Make a confusion matrix and calculate accuracy of predicted vs. true values
|
|
|
80 for a set of samples classified using a sample classifier.
|
|
|
81
|
|
|
82 Parameters
|
|
|
83 ----------
|
|
|
84 predictions : SampleData[ClassifierPredictions]
|
|
|
85 Predicted values to plot on x axis. Should be predictions of
|
|
|
86 categorical data produced by a sample classifier.
|
|
|
87 truth : MetadataColumn[Categorical]
|
|
|
88 Metadata column (true values) to plot on y axis.
|
|
|
89 missing_samples : Str % Choices('error', 'ignore'), optional
|
|
|
90 How to handle missing samples in metadata. "error" will fail if missing
|
|
|
91 samples are detected. "ignore" will cause the feature table and
|
|
|
92 metadata to be filtered, so that only samples found in both files are
|
|
|
93 retained.
|
|
|
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
|
|
|
95 The color palette to use for plotting.
|
|
|
96
|
|
|
97 Returns
|
|
|
98 -------
|
|
|
99 visualization : Visualization
|
|
|
100 ]]></help>
|
|
|
101 <macros>
|
|
|
102 <import>qiime_citation.xml</import>
|
|
|
103 </macros>
|
|
|
104 <expand macro="qiime_citation"/>
|
|
|
105 </tool>
|
