annotate qiime2/qiime_sample-classifier_scatterplot.xml @ 3:558645416841 draft

Uploaded
author florianbegusch
date Sun, 21 Jul 2019 02:21:34 -0400
parents 370e0b6e9826
children a025a4a89e07
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_sample-classifier_scatterplot" name="qiime sample-classifier scatterplot" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Make 2D scatterplot and linear regression of regressor predictions.</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime sample-classifier scatterplot
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-predictions=$ipredictions
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --m-truth-column="$mtruthcolumn"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 --m-truth-file="$metadatafile"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 #if str($pmissingsamples) != 'None':
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 --p-missing-samples=$pmissingsamples
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 --o-visualization=ovisualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 && cp -r out/* '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 && mv '$ovisualization.files_path/index.html' '$ovisualization';
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 cp mtruthfile.qza $mtruthfile
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 <param format="qza,no_unzip.zip" label="--i-predictions: ARTIFACT SampleData[RegressorPredictions] Predicted values to plot on y axis. Must be predictions of numeric data produced by a sample regressor. [required]" name="ipredictions" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 <param label="--m-truth-column: COLUMN MetadataColumn[Numeric] Metadata column (true values) to plot on x axis. [required]" name="mtruthcolumn" optional="False" type="text"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 <option selected="True" value="None">Selection is Optional</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 <option value="error">error</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 <option value="ignore">ignore</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 <param label="--m-truth-file: Metadata file or artifact viewable as metadata." name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 Make 2D scatterplot and linear regression of regressor predictions.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 ###################################################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 Make a 2D scatterplot and linear regression of predicted vs. true values
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 for a set of samples predicted using a sample regressor.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 predictions : SampleData[RegressorPredictions]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 Predicted values to plot on y axis. Must be predictions of numeric data
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 produced by a sample regressor.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 truth : MetadataColumn[Numeric]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 Metadata column (true values) to plot on x axis.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 missing_samples : Str % Choices('error', 'ignore'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 How to handle missing samples in metadata. "error" will fail if missing
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 samples are detected. "ignore" will cause the feature table and
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 metadata to be filtered, so that only samples found in both files are
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 retained.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 visualization : Visualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 </tool>