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comparison qiime2/qiime_sample-classifier_scatterplot.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_sample-classifier_scatterplot" name="qiime sample-classifier scatterplot" version="2019.7"> 2 <tool id="qiime_sample-classifier_scatterplot" name="qiime sample-classifier scatterplot"
3 <description> - Make 2D scatterplot and linear regression of regressor predictions.</description> 3 version="2020.8">
4 <requirements> 4 <description>Make 2D scatterplot and linear regression of regressor predictions.</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime sample-classifier scatterplot 9 qiime sample-classifier scatterplot
9 10
10 --i-predictions=$ipredictions 11 --i-predictions=$ipredictions
11 --m-truth-column="$mtruthcolumn"
12 12
13 --m-truth-file="$mtruthfile" 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
14 40
15 #if str($pmissingsamples) != 'None': 41 #if str($pmissingsamples) != 'None':
16 --p-missing-samples=$pmissingsamples 42 --p-missing-samples=$pmissingsamples
17 #end if 43 #end if
18 44
19 --o-visualization=ovisualization 45 --o-visualization=ovisualization
46
47 #if str($examples) != 'None':
48 --examples=$examples
49 #end if
50
20 ; 51 ;
21 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 52 cp ofeatureimportance.qza $ofeatureimportance
53
54 ;
55 qiime tools export ovisualization.qzv --output-path out
56 && mkdir -p '$ovisualization.files_path'
22 && cp -r out/* '$ovisualization.files_path' 57 && cp -r out/* '$ovisualization.files_path'
23 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 58 && mv '$ovisualization.files_path/index.html' '$ovisualization'
24 ]]></command>
25 <inputs>
26 <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"/>
27 <param label="--m-truth-column: COLUMN MetadataColumn[Numeric] Metadata column (true values) to plot on x axis. [required]" name="mtruthcolumn" optional="False" type="text"/>
28 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
29 <option selected="True" value="None">Selection is Optional</option>
30 <option value="error">error</option>
31 <option value="ignore">ignore</option>
32 </param>
33 59
34 <param label="--m-truth-file: Metadata file or artifact viewable as metadata." name="mtruthfile" type="data" format="tabular,qza,no_unzip.zip" /> 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>
35 73
36 </inputs> 74 <outputs>
37 <outputs> 75 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
38 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 76
39 </outputs> 77 </outputs>
40 <help><![CDATA[ 78
79 <help><![CDATA[
41 Make 2D scatterplot and linear regression of regressor predictions. 80 Make 2D scatterplot and linear regression of regressor predictions.
42 ################################################################### 81 ###############################################################
43 82
44 Make a 2D scatterplot and linear regression of predicted vs. true values 83 Make a 2D scatterplot and linear regression of predicted vs. true values
45 for a set of samples predicted using a sample regressor. 84 for a set of samples predicted using a sample regressor.
46 85
47 Parameters 86 Parameters
58 retained. 97 retained.
59 98
60 Returns 99 Returns
61 ------- 100 -------
62 visualization : Visualization 101 visualization : Visualization
63 ]]></help> 102 ]]></help>
64 <macros> 103 <macros>
65 <import>qiime_citation.xml</import> 104 <import>qiime_citation.xml</import>
66 </macros> 105 </macros>
67 <expand macro="qiime_citation"/> 106 <expand macro="qiime_citation"/>
68 </tool> 107 </tool>