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

Fixes

<?xml version="1.0" ?>
<tool id="qiime_feature-table_merge" name="qiime feature-table merge" version="2019.4">
	<description> - Combine multiple tables</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime feature-table merge

#if $input_files_itables:
#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 + ' --i-tables=' + d['additional_input'].__getattr__('file_name')
	#end for
	#return $file_list
#end def
 --i-tables=$list_dict_to_string($input_files_itables)
#end if


#if str($poverlapmethod) != 'None':
 --p-overlap-method=$poverlapmethod
#end if


--o-merged-table=omergedtable
;
cp omergedtable.qza $omergedtable
	]]></command>
	<inputs>
		<repeat name="input_files_itables" optional="False" title="--i-tables">
			<param format="qza,no_unzip.zip" label="--i-tables: PATH List[FeatureTable[Frequency]] The collection of feature tables to be merged.  [required]" name="additional_input" type="data"/>
		</repeat>

		<param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="error_on_overlapping_sample">error_on_overlapping_sample</option>
			<option value="error_on_overlapping_feature">error_on_overlapping_feature</option>
			<option value="sum">sum</option>
		</param>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable"/>
	</outputs>
	<help><![CDATA[
Combine multiple tables
#######################

Combines feature tables using the `overlap_method` provided.

Parameters
----------
tables : List[FeatureTable[Frequency]]
    The collection of feature tables to be merged.
overlap_method : Str % Choices('error_on_overlapping_sample', 'error_on_overlapping_feature', 'sum'), optional
    Method for handling overlapping ids.

Returns
-------
merged_table : FeatureTable[Frequency]
    The resulting merged feature table.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>