<?xml version="1.0" ?>
<tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects" version="2018.4">
	<description> - Linear mixed effects modeling</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime longitudinal linear-mixed-effects --p-state-column="$pstatecolumn"

	#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) --p-individual-id-column="$pindividualidcolumn" --p-metric="$pmetric"
	#if str($itable) != 'None':
	 --i-table=$itable
	#end if

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if
	 --o-visualization=ovisualization
	#if $pci:
	 --p-ci=$pci
	#end if

	#if str($ppalette) != 'None':
	 --p-palette=$ppalette
	#end if

	#if str($pgroupcolumns):
	 --p-group-columns="$pgroupcolumns"
	#end if

	#if $plowess:
	  --p-lowess
	#else
	  --p-no-lowess
	#end if

	#if str($prandomeffects):
	 --p-random-effects="$prandomeffects"
	#end if
	;

	qiime tools export ovisualization.qzv --output-dir 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: FeatureTable[RelativeFrequency] Feature table to optionally use for paired comparisons.  [optional]" name="itable" optional="True" type="data"/>

		<repeat name="input_files_mmetadatafile" optional="False" 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. Sample metadata file containing individual_id_column.  [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

		<param label="--p-metric: Dependent variable column name. Must be a column name located in the metadata or feature table files.  [required]" name="pmetric" optional="False" type="text"/>

		<param label="--p-state-column: Metadata column containing state (e.g., Time) across which samples are paired. [required]" name="pstatecolumn" optional="False" type="text"/>

		<param label="--p-individual-id-column: Metadata column containing IDs for individual subjects.  [required]" name="pindividualidcolumn" optional="False" type="text"/>
		<param label="--p-group-columns: Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine mean structure of 'metric'.  [optional]" name="pgroupcolumns" optional="True" type="text"/>

		<param label="--p-random-effects: Comma-separated list (without spaces) of metadata columns to use as independent covariates used to determine the variance and covariance structure (random effects) of 'metric'. To add a random slope, the same value passed to 'state_column' should be passed here. A random intercept for each individual is set by default and does not need to be passed here.  [optional]" name="prandomeffects" optional="True" type="text"/>

		<param label="--p-palette: Color palette to use for generating
                                  boxplots.  [default: Set1]" name="ppalette" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="Accent">Accent</option>
			<option value="tab20">tab20</option>
			<option value="Pastel2">Pastel2</option>
			<option value="plasma">plasma</option>
			<option value="viridis">viridis</option>
			<option value="rainbow">rainbow</option>
			<option value="Pastel1">Pastel1</option>
			<option value="inferno">inferno</option>
			<option value="magma">magma</option>
			<option value="tab20b">tab20b</option>
			<option value="Set3">Set3</option>
			<option value="Set2">Set2</option>
			<option value="Dark2">Dark2</option>
			<option value="Set1">Set1</option>
			<option value="tab10">tab10</option>
			<option value="tab20c">tab20c</option>
			<option value="terrain">terrain</option>
			<option value="Paired">Paired</option>
		</param>

		<param label="--p-lowess: --p-no-lowess      Estimate locally weighted scatterplot smoothing. Note that this will eliminate confidence interval plotting.  [default: False]" name="plowess" checked="False" type="boolean"/>
		<param label="--p-ci: Size of the confidence interval for the regression estimate.  [default: 95]" name="pci" optional="True" type="integer" value="95"/>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
	</outputs>
	<help>
		<![CDATA[
Linear mixed effects modeling
------------------------------

Linear mixed effects models evaluate the contribution of exogenous
covariates "group_columns" and "random_effects" to a single dependent
variable, "metric". Perform LME and plot line plots of each group column. A
feature table artifact is required input, though whether "metric" is
derived from the feature table or metadata is optional.

Parameters
----------
table : FeatureTable[RelativeFrequency], optional
    Feature table to optionally use for paired comparisons.
metadata : Metadata
    Sample metadata file containing individual_id_column.
metric : Str
    Dependent variable column name. Must be a column name located in the
    metadata or feature table files.
state_column : Str
    Metadata column containing state (e.g., Time) across which samples are
    paired.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
group_columns : Str, optional
    Comma-separated list (without spaces) of metadata columns to use as
    independent covariates used to determine mean structure of "metric".
random_effects : Str, optional
    Comma-separated list (without spaces) of metadata columns to use as
    independent covariates used to determine the variance and covariance
    structure (random effects) of "metric". To add a random slope, the same
    value passed to "state_column" should be passed here. A random
    intercept for each individual is set by default and does not need to be
    passed here.
palette : Str % Choices({'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'inferno', 'magma', 'plasma', 'rainbow', 'tab10', 'tab20', 'tab20b', 'tab20c', 'terrain', 'viridis'}), optional
    Color palette to use for generating boxplots.
lowess : Bool, optional
    Estimate locally weighted scatterplot smoothing. Note that this will
    eliminate confidence interval plotting.
ci : Float % Range(0, 100), optional
    Size of the confidence interval for the regression estimate.

Returns
-------
visualization : Visualization
		\
		]]>
	</help>
</tool>