Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_sample-classifier_scatterplot.xml @ 0:370e0b6e9826 draft
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| author | florianbegusch |
|---|---|
| date | Wed, 17 Jul 2019 03:05:17 -0400 |
| parents | |
| children | a025a4a89e07 |
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| -1:000000000000 | 0:370e0b6e9826 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_sample-classifier_scatterplot" name="qiime sample-classifier scatterplot" version="2019.4"> | |
| 3 <description> - Make 2D scatterplot and linear regression of regressor predictions.</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2019.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command><![CDATA[ | |
| 8 qiime sample-classifier scatterplot | |
| 9 | |
| 10 --i-predictions=$ipredictions | |
| 11 --m-truth-column="$mtruthcolumn" | |
| 12 | |
| 13 --m-truth-file="$metadatafile" | |
| 14 | |
| 15 #if str($pmissingsamples) != 'None': | |
| 16 --p-missing-samples=$pmissingsamples | |
| 17 #end if | |
| 18 | |
| 19 --o-visualization=ovisualization | |
| 20 ; | |
| 21 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' | |
| 22 && cp -r out/* '$ovisualization.files_path' | |
| 23 && mv '$ovisualization.files_path/index.html' '$ovisualization'; | |
| 24 cp mtruthfile.qza $mtruthfile | |
| 25 ]]></command> | |
| 26 <inputs> | |
| 27 <param format="qza,no_unzip.zip" label="--i-predictions: ARTIFACT SampleData[RegressorPredictions] Predicted values to plot on y axis. Must be predictions of numeric data produced by a sample regressor. [required]" name="ipredictions" optional="False" type="data"/> | |
| 28 <param label="--m-truth-column: COLUMN MetadataColumn[Numeric] Metadata column (true values) to plot on x axis. [required]" name="mtruthcolumn" optional="False" type="text"/> | |
| 29 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select"> | |
| 30 <option selected="True" value="None">Selection is Optional</option> | |
| 31 <option value="error">error</option> | |
| 32 <option value="ignore">ignore</option> | |
| 33 </param> | |
| 34 | |
| 35 <param label="--m-truth-file: Metadata file or artifact viewable as metadata." name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" /> | |
| 36 | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> | |
| 40 </outputs> | |
| 41 <help><![CDATA[ | |
| 42 Make 2D scatterplot and linear regression of regressor predictions. | |
| 43 ################################################################### | |
| 44 | |
| 45 Make a 2D scatterplot and linear regression of predicted vs. true values | |
| 46 for a set of samples predicted using a sample regressor. | |
| 47 | |
| 48 Parameters | |
| 49 ---------- | |
| 50 predictions : SampleData[RegressorPredictions] | |
| 51 Predicted values to plot on y axis. Must be predictions of numeric data | |
| 52 produced by a sample regressor. | |
| 53 truth : MetadataColumn[Numeric] | |
| 54 Metadata column (true values) to plot on x axis. | |
| 55 missing_samples : Str % Choices('error', 'ignore'), optional | |
| 56 How to handle missing samples in metadata. "error" will fail if missing | |
| 57 samples are detected. "ignore" will cause the feature table and | |
| 58 metadata to be filtered, so that only samples found in both files are | |
| 59 retained. | |
| 60 | |
| 61 Returns | |
| 62 ------- | |
| 63 visualization : Visualization | |
| 64 ]]></help> | |
| 65 <macros> | |
| 66 <import>qiime_citation.xml</import> | |
| 67 </macros> | |
| 68 <expand macro="qiime_citation"/> | |
| 69 </tool> |