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view qiime2/qiime_sample-classifier_confusion-matrix.xml @ 10:21c7954105a9 draft
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author | florianbegusch |
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date | Sun, 25 Aug 2019 10:26:27 -0400 |
parents | f190567fe3f6 |
children | a0a8d77a991c |
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<?xml version="1.0" ?> <tool id="qiime_sample-classifier_confusion-matrix" name="qiime sample-classifier confusion-matrix" version="2019.7"> <description> - Make a confusion matrix from sample classifier predictions.</description> <requirements> <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier confusion-matrix --i-predictions=$ipredictions --m-truth-column="$mtruthcolumn" --m-truth-file=mtruthfile #if str($pmissingsamples) != 'None': --p-missing-samples=$pmissingsamples #end if #if str($ppalette) != 'None': --p-palette=$ppalette #end if --o-visualization=ovisualization ; qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' && cp -r out/* '$ovisualization.files_path' && mv '$ovisualization.files_path/index.html' '$ovisualization'; cp mtruthfile.qza $mtruthfile ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-predictions: ARTIFACT SampleData[ClassifierPredictions] Predicted values to plot on x axis. Should be predictions of categorical data produced by a sample classifier. [required]" name="ipredictions" optional="False" type="data"/> <param label="--m-truth-column: COLUMN MetadataColumn[Categorical] Metadata column (true values) to plot on y axis. [required]" name="mtruthcolumn" optional="False" type="text"/> <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option> <option value="error">error</option> <option value="ignore">ignore</option> </param> <param label="--p-palette: " name="ppalette" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option> <option value="YellowOrangeBrown">YellowOrangeBrown</option> <option value="YellowOrangeRed">YellowOrangeRed</option> <option value="OrangeRed">OrangeRed</option> <option value="PurpleRed">PurpleRed</option> <option value="RedPurple">RedPurple</option> <option value="BluePurple">BluePurple</option> <option value="GreenBlue">GreenBlue</option> <option value="PurpleBlue">PurpleBlue</option> <option value="YellowGreen">YellowGreen</option> <option value="summer">summer</option> <option value="copper">copper</option> <option value="viridis">viridis</option> <option value="plasma">plasma</option> <option value="inferno">inferno</option> <option value="magma">magma</option> <option value="sirocco">sirocco</option> <option value="drifting">drifting</option> <option value="melancholy">melancholy</option> <option value="enigma">enigma</option> <option value="eros">eros</option> <option value="spectre">spectre</option> <option value="ambition">ambition</option> <option value="mysteriousstains">mysteriousstains</option> <option value="daydream">daydream</option> <option value="solano">solano</option> <option value="navarro">navarro</option> <option value="dandelions">dandelions</option> <option value="deepblue">deepblue</option> <option value="verve">verve</option> <option value="greyscale">greyscale</option> </param> </inputs> <outputs> <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> <data format="qza" label="${tool.name} on ${on_string}: truthfile.qza" name="mtruthfile"/> </outputs> <help><![CDATA[ Make a confusion matrix from sample classifier predictions. ########################################################### Make a confusion matrix and calculate accuracy of predicted vs. true values for a set of samples classified using a sample classifier. Parameters ---------- predictions : SampleData[ClassifierPredictions] Predicted values to plot on x axis. Should be predictions of categorical data produced by a sample classifier. truth : MetadataColumn[Categorical] Metadata column (true values) to plot on y axis. missing_samples : Str % Choices('error', 'ignore'), optional How to handle missing samples in metadata. "error" will fail if missing samples are detected. "ignore" will cause the feature table and metadata to be filtered, so that only samples found in both files are retained. palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional The color palette to use for plotting. Returns ------- visualization : Visualization ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>