view qiime2/qiime_diversity_beta-group-significance.xml @ 6:de4c22a52df4 draft

Fixes

<?xml version="1.0" ?>
<tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance" version="2019.4">
	<description> - Beta diversity group significance</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime diversity beta-group-significance

--i-distance-matrix=$idistancematrix
--m-metadata-column="$mmetadatacolumn"



#if $metadatafile:
 --m-metadata-file=$metadatafile
#end if


#if str($pmethod) != 'None':
 --p-method=$pmethod
#end if

#if $ppairwise:
 --p-pairwise
#end if

#if str($ppermutations):
 --p-permutations=$ppermutations
#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'
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix     Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
		<param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] Categorical sample metadata column.          [required]" name="mmetadatacolumn" optional="False" type="text"/>
		<param label="--p-method: " name="pmethod" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="permanova">permanova</option>
			<option value="anosim">anosim</option>
			<option value="permdisp">permdisp</option>
		</param>
		<param label="--p-pairwise: --p-no-pairwise Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column.                                [default: False]" name="ppairwise" selected="False" type="boolean"/>
		<param label="--p-permutations: INTEGER The number of permutations to be run when computing p-values.                                [default: 999]" name="ppermutations" optional="True" type="integer" value="999"/>

		<param label="--m-metadata-file METADATA [required]" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" optional="False" />
	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
	</outputs>
	<help><![CDATA[
Beta diversity group significance
#################################

Determine whether groups of samples are significantly different from one
another using a permutation-based statistical test.

Parameters
----------
distance_matrix : DistanceMatrix
    Matrix of distances between pairs of samples.
metadata : MetadataColumn[Categorical]
    Categorical sample metadata column.
method : Str % Choices('permanova', 'anosim', 'permdisp'), optional
    The group significance test to be applied.
pairwise : Bool, optional
    Perform pairwise tests between all pairs of groups in addition to the
    test across all groups. This can be very slow if there are a lot of
    groups in the metadata column.
permutations : Int, optional
    The number of permutations to be run when computing p-values.

Returns
-------
visualization : Visualization
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>