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comparison qiime2/qiime_sample-classifier_confusion-matrix.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_sample-classifier_confusion-matrix" name="qiime sample-classifier confusion-matrix" version="2019.4">
3 <description> - Make a confusion matrix from sample classifier predictions.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
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>