<?xml version="1.0" ?>
<tool id="qiime_feature-table_group" name="qiime feature-table group" version="2019.4">
	<description> - Group samples or features by a metadata column</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime feature-table group

--i-table=$itable
--p-axis=$paxis
--m-metadata-column="$mmetadatacolumn"
--p-mode=$pmode


#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-grouped-table=ogroupedtable
;
cp ogroupedtable.qza $ogroupedtable
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The table to group samples or features on.   [required]" name="itable" optional="False" type="data"/>
		<param label="--p-axis: " name="paxis" optional="False" type="select">
			<option value="feature">feature</option>
			<option value="sample">sample</option>
		</param>
		<param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] A column defining the groups. Each unique value will become a new ID for the table on the given `axis`. [required]" name="mmetadatacolumn" optional="False" type="text"/>
		<param label="--p-mode: " name="pmode" optional="False" type="select">
			<option value="median-ceiling">median-ceiling</option>
			<option value="mean-ceiling">mean-ceiling</option>
			<option value="sum">sum</option>
		</param>

		<repeat name="input_files_mmetadatafile" optional="True" 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. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: groupedtable.qza" name="ogroupedtable"/>
	</outputs>
	<help><![CDATA[
Group samples or features by a metadata column
##############################################

Group samples or features in a feature table using metadata to define the
mapping of IDs to a group.

Parameters
----------
table : FeatureTable[Frequency]
    The table to group samples or features on.
axis : Str % Choices('sample', 'feature')
    Along which axis to group. Each ID in the given axis must exist in
    `metadata`.
metadata : MetadataColumn[Categorical]
    A column defining the groups. Each unique value will become a new ID
    for the table on the given `axis`.
mode : Str % Choices('median-ceiling', 'mean-ceiling', 'sum')
    How to combine samples or features within a group. `sum` will sum the
    frequencies across all samples or features within a group; `mean-
    ceiling` will take the ceiling of the mean of these frequencies;
    `median-ceiling` will take the ceiling of the median of these
    frequencies.

Returns
-------
grouped_table : FeatureTable[Frequency]
    A table that has been grouped along the given `axis`. IDs on that axis
    are replaced by values in the `metadata` column.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>