Mercurial > repos > florianbegusch > qiime2_suite
view qiime2/qiime_sample-classifier_classify-samples-from-dist.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_classify-samples-from-dist" name="qiime sample-classifier classify-samples-from-dist" version="2019.7"> <description> - Run k-nearest-neighbors on a labeled distance matrix.</description> <requirements> <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier classify-samples-from-dist --i-distance-matrix=$idistancematrix --m-metadata-column="$mmetadatacolumn" #if str($pk): --p-k=$pk #end if #if str($ppalette) != 'None': --p-palette=$ppalette #end if #if $metadatafile: --m-metadata-file=$metadatafile #end if --o-predictions=opredictions --o-accuracy-results=oaccuracyresults ; cp opredictions.qza $opredictions; qiime tools export --input-path oaccuracyresults.qzv --output-path out && mkdir -p '$oaccuracyresults.files_path' && cp -r out/* '$oaccuracyresults.files_path' && mv '$oaccuracyresults.files_path/index.html' '$oaccuracyresults' ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix a distance matrix [required]" name="idistancematrix" optional="False" type="data"/> <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text"/> <param label="--p-k: INTEGER Number of nearest neighbors [default: 1]" name="pk" optional="True" type="integer" value="1"/> <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> <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" /> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/> <data format="html" label="${tool.name} on ${on_string}: accuracyresults.qzv" name="oaccuracyresults"/> </outputs> <help><![CDATA[ Run k-nearest-neighbors on a labeled distance matrix. ##################################################### Run k-nearest-neighbors on a labeled distance matrix. Return cross- validated (leave one out) predictions and accuracy. k = 1 by default Parameters ---------- distance_matrix : DistanceMatrix a distance matrix metadata : MetadataColumn[Categorical] Categorical metadata column to use as prediction target. k : Int, optional Number of nearest neighbors 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 ------- predictions : SampleData[ClassifierPredictions] leave one out predictions for each sample accuracy_results : Visualization Accuracy results visualization. ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>