Mercurial > repos > florianbegusch > qiime2_suite

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

--i-alpha-diversity=$ialphadiversity


#def list_dict_to_string(list_dict):
#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
#for d in list_dict[1:]:
	#set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
#end for
#return $file_list
#end def

--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)

--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-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample.  [required]" name="ialphadiversity" optional="False" type="data"/>

		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>
	</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>
author	florianbegusch
date	Wed, 17 Jul 2019 03:05:17 -0400
parents
children	51025741f326