<?xml version="1.0" ?>
<tool id="qiime_feature-table_group" name="qiime feature-table group" version="2018.4">
	<description> - Group samples or features by a metadata column</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime feature-table group --i-table=$itable

	#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 + ',' + d['additional_input'].__getattr__('file_name')
		#end for
		#return $file_list

	#end def
	 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-mode=$pmode --m-metadata-column="$mmetadatacolumn" --p-axis=$paxis
	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if
	 --o-grouped-table=ogroupedtable;
	cp ogroupedtable.qza $ogroupedtable;
	]]>
	</command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The table to group samples or features on. [required]" name="itable" optional="False" type="data"/>

		<param label="--p-axis: Along which axis to group. Each ID in the
                                  given axis must exist in `metadata`.
                                  [required]" name="paxis" optional="False" type="select">
			<option value="sample">sample</option>
			<option value="feature">feature</option>
		</param>

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

		<param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. 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: 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.  [required]" 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>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: grouped-table.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({'feature', 'sample'})
    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({'mean-ceiling', 'median-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>