|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_sample-classifier_scatterplot" name="qiime sample-classifier scatterplot"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Make 2D scatterplot and linear regression of regressor predictions.</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime sample-classifier scatterplot
|
|
|
10
|
|
|
11 --i-predictions=$ipredictions
|
|
|
12
|
|
|
13 #if str($mtruthfile) != 'None':
|
|
|
14 --m-truth-file=$mtruthfile
|
|
|
15 #end if
|
|
|
16
|
|
|
17 #if '__ob__' in str($mtruthcolumn):
|
|
|
18 #set $mtruthcolumn_temp = $mtruthcolumn.replace('__ob__', '[')
|
|
|
19 #set $mtruthcolumn = $mtruthcolumn_temp
|
|
|
20 #end if
|
|
|
21 #if '__cb__' in str($mtruthcolumn):
|
|
|
22 #set $mtruthcolumn_temp = $mtruthcolumn.replace('__cb__', ']')
|
|
|
23 #set $mtruthcolumn = $mtruthcolumn_temp
|
|
|
24 #end if
|
|
|
25 #if 'X' in str($mtruthcolumn):
|
|
|
26 #set $mtruthcolumn_temp = $mtruthcolumn.replace('X', '\\')
|
|
|
27 #set $mtruthcolumn = $mtruthcolumn_temp
|
|
|
28 #end if
|
|
|
29 #if '__sq__' in str($mtruthcolumn):
|
|
|
30 #set $mtruthcolumn_temp = $mtruthcolumn.replace('__sq__', "'")
|
|
|
31 #set $mtruthcolumn = $mtruthcolumn_temp
|
|
|
32 #end if
|
|
|
33 #if '__db__' in str($mtruthcolumn):
|
|
|
34 #set $mtruthcolumn_temp = $mtruthcolumn.replace('__db__', '"')
|
|
|
35 #set $mtruthcolumn = $mtruthcolumn_temp
|
|
|
36 #end if
|
|
|
37
|
|
|
38 --m-truth-column=$mtruthcolumn
|
|
|
39
|
|
|
40
|
|
|
41 #if str($pmissingsamples) != 'None':
|
|
|
42 --p-missing-samples=$pmissingsamples
|
|
|
43 #end if
|
|
|
44
|
|
|
45 --o-visualization=ovisualization
|
|
|
46
|
|
|
47 #if str($examples) != 'None':
|
|
|
48 --examples=$examples
|
|
|
49 #end if
|
|
|
50
|
|
|
51 ;
|
|
|
52 cp ofeatureimportance.qza $ofeatureimportance
|
|
|
53
|
|
|
54 ;
|
|
|
55 qiime tools export ovisualization.qzv --output-path out
|
|
|
56 && mkdir -p '$ovisualization.files_path'
|
|
|
57 && cp -r out/* '$ovisualization.files_path'
|
|
|
58 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
59
|
|
|
60 ]]></command>
|
|
|
61 <inputs>
|
|
|
62 <param format="qza,no_unzip.zip" label="--i-predictions: ARTIFACT SampleData[RegressorPredictions] Predicted values to plot on y axis. Must be predictions of numeric data produced by a sample regressor. [required]" name="ipredictions" optional="False" type="data" />
|
|
|
63 <param label="--m-truth-file: METADATA" name="mtruthfile" optional="False" type="data" />
|
|
|
64 <param label="--m-truth-column: COLUMN MetadataColumn[Numeric] Metadata column (true values) to plot on x axis. [required]" name="mtruthcolumn" optional="False" type="text" />
|
|
|
65 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
|
|
|
66 <option selected="True" value="None">Selection is Optional</option>
|
|
|
67 <option value="error">error</option>
|
|
|
68 <option value="ignore">ignore</option>
|
|
|
69 </param>
|
|
|
70 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
71
|
|
|
72 </inputs>
|
|
|
73
|
|
|
74 <outputs>
|
|
|
75 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
|
|
|
76
|
|
|
77 </outputs>
|
|
|
78
|
|
|
79 <help><![CDATA[
|
|
|
80 Make 2D scatterplot and linear regression of regressor predictions.
|
|
|
81 ###############################################################
|
|
|
82
|
|
|
83 Make a 2D scatterplot and linear regression of predicted vs. true values
|
|
|
84 for a set of samples predicted using a sample regressor.
|
|
|
85
|
|
|
86 Parameters
|
|
|
87 ----------
|
|
|
88 predictions : SampleData[RegressorPredictions]
|
|
|
89 Predicted values to plot on y axis. Must be predictions of numeric data
|
|
|
90 produced by a sample regressor.
|
|
|
91 truth : MetadataColumn[Numeric]
|
|
|
92 Metadata column (true values) to plot on x axis.
|
|
|
93 missing_samples : Str % Choices('error', 'ignore'), optional
|
|
|
94 How to handle missing samples in metadata. "error" will fail if missing
|
|
|
95 samples are detected. "ignore" will cause the feature table and
|
|
|
96 metadata to be filtered, so that only samples found in both files are
|
|
|
97 retained.
|
|
|
98
|
|
|
99 Returns
|
|
|
100 -------
|
|
|
101 visualization : Visualization
|
|
|
102 ]]></help>
|
|
|
103 <macros>
|
|
|
104 <import>qiime_citation.xml</import>
|
|
|
105 </macros>
|
|
|
106 <expand macro="qiime_citation"/>
|
|
|
107 </tool> |
