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comparison qiime2-2020.8/qiime_sample-classifier_scatterplot.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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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>