view qiime2/qiime_gneiss_lme-regression.xml @ 8:d66c7509e8f9 draft

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<?xml version="1.0" ?>
<tool id="qiime_gneiss_lme-regression" name="qiime gneiss lme-regression" version="2019.4">
	<description> - Simplicial Linear mixed effects regression</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime gneiss lme-regression

--i-table=$itable
--i-tree=$itree
--p-formula="$pformula"
--p-groups="$pgroups"


#if $input_files_mmetadatafile:
#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 + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
	#end for
	#return $file_list
#end def
 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
#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-table: ARTIFACT FeatureTable[Balance] The feature table containing the samples in which simplicial regression with mixed effect will be performed.                                   [required]" name="itable" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT    A hierarchy of feature identifiers where each tip Hierarchy          corresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                        [required]" name="itree" optional="False" type="data"/>
		<param label="--p-formula: TEXT     Statistical formula specifying the statistical model. In other words, a list of the metadata categories that will be used in the linear mixed effect model, typically separated by '+'. For more information see https://patsy.readthedocs.io/en/latest/API-reference.ht ml                                           [required]" name="pformula" optional="False" type="text"/>
		<param label="--p-groups: TEXT                                                   [required]" name="pgroups" optional="False" type="text"/>

		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
			<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[
Simplicial Linear mixed effects regression
##########################################

Build and run linear mixed effects model on balances. Use LME over OLS when
you have repeated measurements such as (timeseries).

Parameters
----------
table : FeatureTable[Balance]
    The feature table containing the samples in which simplicial regression
    with mixed effect will be performed.
tree : Hierarchy
    A hierarchy of feature identifiers where each tip corresponds to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.
metadata : Metadata
    Metadata information that contains the covariates of interest.
formula : Str
    Statistical formula specifying the statistical model. In other words, a
    list of the metadata categories that will be used in the linear mixed
    effect model, typically separated by "+". For more information see
    https://patsy.readthedocs.io/en/latest/API-reference.html
groups : Str
	\

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