<?xml version="1.0" ?>
<tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility" version="2018.4">
	<description> - Volatility analysis</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime longitudinal volatility --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-default-group-column="$pdefaultgroupcolumn"
	 --p-individual-id-column="$pindividualidcolumn"
	  --p-default-metric="$pdefaultmetric"
	#if str($itable) != 'None':
	 --i-table=$itable
	#end if

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

	#if str($pyscale) != 'None':
	 --p-yscale=$pyscale
	#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>
		<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-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-default-group-column: The default metadata column on which to
                                  separate groups for comparison (all
                                  categorical metadata columns will be
                                  available in the visualization).  [optional]" name="pdefaultgroupcolumn" optional="False" type="text"/>

		<param label="--p-default-metric: Numeric metadata or artifact column to test
                                  by default (all numeric metadata columns
                                  will be available in the visualization).
                                  [optional]" name="pdefaultmetric" optional="False" type="text"/>

		<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"/>

		<param label="--p-yscale: y-axis scaling strategy to apply.  [default:
                                  linear]" name="pyscale" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="pow">log</option>
			<option value="linear">logit</option>
			<option value="sqrt">symlog</option>
			<option value="log">linear</option>
		</param>

		<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[
Volatility analysis
--------------------

Plot an interactive control chart of a single dependent variable, "metric",
across multiple groups contained in sample metadata column "group_column".

Parameters
----------
table : FeatureTable[RelativeFrequency], optional
    Feature table to optionally use for paired comparisons.
metadata : Metadata
    Sample metadata file containing individual_id_column.
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.
default_group_column : Str, optional
    The default metadata column on which to separate groups for comparison
    (all categorical metadata columns will be available in the
    visualization).
default_metric : Str, optional
    Numeric metadata or artifact column to test by default (all numeric
    metadata columns will be available in the visualization).
yscale : Str % Choices({'linear', 'log', 'pow', 'sqrt'}), optional
    y-axis scaling strategy to apply.

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