<?xml version="1.0" ?>
<tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2018.4">
	<description>- Visualize taxonomy with an interactive bar plot</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime taxa barplot

	#if str( $id_to_taxonomy_fp.selector ) == 'history'
		#set $tax = $id_to_taxonomy_fp.taxonomy_fp
		--i-taxonomy '$tax'
	#else:
		#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
		--i-taxonomy '$tax'
	#end if

	#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)
	 --i-table=$itable --o-visualization=ovisualization

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#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[Frequency] Feature table to visualize at various taxonomic levels.  [required]" name="itable" optional="False" type="data"/>

		<conditional name="id_to_taxonomy_fp" optional="True">
		   <param name="selector" type="select" label="Reference taxonomy to query">
			  <option value="cached">Public databases</option>
			  <option value="history">Databases from your history</option>
		   </param>
		   <when value="cached">
			  <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
				 <options from_data_table="qiime_taxonomy" />
			  </param>
		   </when>
		   <when value="history">
			  <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
		   </when>
		</conditional>

		<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. The sample metadata.  [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

		<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[
Visualize taxonomy with an interactive bar plot
------------------------------------------------

This visualizer produces an interactive barplot visualization of
taxonomies. Interactive features include multi-level sorting, plot
recoloring, sample relabeling, and SVG figure export.

Parameters
----------
table : FeatureTable[Frequency]
    Feature table to visualize at various taxonomic levels.
taxonomy : FeatureData[Taxonomy]
    Taxonomic annotations for features in the provided feature table. All
    features in the feature table must have a corresponding taxonomic
    annotation. Taxonomic annotations that are not present in the feature
    table will be ignored.
metadata : Metadata
    The sample metadata.

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