view qiime2/qiime_sample-classifier_classify-samples-from-dist.xml @ 8:d66c7509e8f9 draft

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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="2019.4">
	<description> - Run k-nearest-neighbors on a labeled distance matrix.</description>
	<requirements>
		<requirement type="package" version="2019.4">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>