view qiime2/qiime_feature-table_summarize.xml @ 4:914fa4daf16a draft

Fixes

<?xml version="1.0" ?>
<tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" version="2019.4">
	<description> - Summarize table</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime feature-table summarize

--i-table=$itable


#if $m_sample_metadatafile:
#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($m_sample_metadatafile)
#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 | RelativeFrequency | PresenceAbsence]   The feature table to be summarized.          [required]" name="itable" optional="False" type="data"/>

		<repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file">
			<param label="--m-sample-metadata-file: (multiple arguments will be merged)  The sample metadata. [required]" 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[
Summarize table
###############

Generate visual and tabular summaries of a feature table.

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

Returns
-------
visualization : Visualization
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>