<?xml version="1.0" ?>
<tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences" version="2018.4">
	<description> - Paired difference testing and boxplots</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime longitudinal pairwise-differences --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-group-column="$pgroupcolumn" --p-individual-id-column="$pindividualidcolumn" --p-state-1="$pstate1" --p-state-2="$pstate2" --p-metric="$pmetric"
	#if str($itable) != 'None':
	 --i-table=$itable
	#end if

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

	#if str($preplicatehandling) != 'None':
	 --p-replicate-handling=$preplicatehandling
	#end if

	#if $pparametric:
	  --p-parametric
	#else
		--p-no-parametric
	#end if

	#if str($ppalette) != 'None':
	 --p-palette=$ppalette
	#end if
	 --o-visualization=ovisualization;
	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-group-column: Metadata column on which to separate groups for comparison  [required]" name="pgroupcolumn" optional="False" type="text"/>
		<param label="--p-metric: Numerical metadata or artifact column to test.  [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-state-1: Baseline state column value.  [required]" name="pstate1" optional="False" type="text"/>
		<param label="--p-state-2: State column value to pair with baseline. [required]" name="pstate2" optional="False" type="text"/>

		<param label="--p-individual-id-column: Metadata column containing subject IDs to use for pairing samples. WARNING: if replicates exist for an individual ID at either state_1 or state_2, that subject will be dropped and reported in standard output by default. Set replicate_handling='random' to instead randomly select one member. [required]" name="pindividualidcolumn" optional="False" type="text"/>
		<param label="--p-parametric: --p-no-parametric Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests. [default: False]" name="pparametric" checked="False" type="boolean"/>

		<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-replicate-handling: Choose how replicate samples are handled. If
                                  replicates are detected, 'error' causes
                                  method to fail; 'drop' will discard all
                                  replicated samples; 'random' chooses one
                                  representative at random from among
                                  replicates.  [default: error]" name="preplicatehandling" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="error">error</option>
			<option value="random">random</option>
			<option value="drop">drop</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[
Paired difference testing and boxplots
---------------------------------------

Performs paired difference testing between samples from each subject.
Sample pairs may represent a typical intervention study, e.g., samples
collected pre- and post-treatment; paired samples from two different
timepoints (e.g., in a longitudinal study design), or identical samples
receiving different two different treatments. This action tests whether the
change in a numeric metadata value "metric" differs from zero and differs
between groups (e.g., groups of subjects receiving different treatments),
and produces boxplots of paired difference distributions for each group. 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.
group_column : Str
    Metadata column on which to separate groups for comparison
metric : Str
    Numerical metadata or artifact column to test.
state_column : Str
    Metadata column containing state (e.g., Time) across which samples are
    paired.
state_1 : Str
    Baseline state column value.
state_2 : Str
    State column value to pair with baseline.
individual_id_column : Str
    Metadata column containing subject IDs to use for pairing samples.
    WARNING: if replicates exist for an individual ID at either state_1 or
    state_2, that subject will be dropped and reported in standard output
    by default. Set replicate_handling="random" to instead randomly select
    one member.
parametric : Bool, optional
    Perform parametric (ANOVA and t-tests) or non-parametric (Kruskal-
    Wallis, Wilcoxon, and Mann-Whitney U tests) statistical tests.
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.
replicate_handling : Str % Choices({'drop', 'error', 'random'}), optional
    Choose how replicate samples are handled. If replicates are detected,
    "error" causes method to fail; "drop" will discard all replicated
    samples; "random" chooses one representative at random from among
    replicates.

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