view qiime2/qiime_taxa_barplot.xml @ 5:a025a4a89e07 draft

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<?xml version="1.0" ?>
<tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2019.4">
	<description> - Visualize taxonomy with an interactive bar plot</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime taxa barplot

--i-table=$itable
--i-taxonomy=$itaxonomy

#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[Frequency] Feature table to visualize at various taxonomic levels.                                    [required]" name="itable" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT 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.                           [required]" name="itaxonomy" optional="False" type="data"/>

		<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[
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>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>