comparison qiime_feature-table_summarize.xml @ 0:09b7bcb72fa7 draft

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0:09b7bcb72fa7

<?xml version="1.0" ?>
<tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" version="2018.4">
	<description> - Summarize table</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime feature-table summarize --i-table=$itable

	#if $input_files_msamplemetadatafile:

	#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 $file_list
	#end def
	 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
	#end if

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#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[Frequency | PresenceAbsence | RelativeFrequency] The feature table to be summarized. [required]" name="itable" optional="False" type="data"/>
		<repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
			<param label="--m-sample-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata.  [optional]" 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[
Summarize table
----------------

Generate visual and tabular summaries of a feature table.

Parameters
----------
table : FeatureTable[Frequency | PresenceAbsence | RelativeFrequency]
    The feature table to be summarized.
sample_metadata : Metadata, optional
    The sample metadata.

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