view qiime2/qiime_feature-table_filter-seqs.xml @ 8:d66c7509e8f9 draft

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<?xml version="1.0" ?>
<tool id="qiime_feature-table_filter-seqs" name="qiime feature-table filter-seqs" version="2019.4">
	<description> - Filter features from sequences</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime feature-table filter-seqs

--i-data=$idata


#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


#if str($itable) != 'None':
 --i-table=$itable
#end if

#if '__sq__' in str($pwhere):
  #set $pwhere_temp = $pwhere.replace('__sq__', "'")
  #set $pwhere = $pwhere_temp
#end if

#if str($pwhere):
 --p-where="$pwhere"
#end if

#if $pexcludeids:
 --p-exclude-ids
#end if

--o-filtered-data=ofiltereddata
;
cp ofiltereddata.qza $ofiltereddata
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence] The sequences from which features should be filtered. [required]" name="idata" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Table containing feature ids used for id-based filtering.                                   [optional]" name="itable" optional="True" type="data"/>
		<param label="--p-where: TEXT       SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences will be retained.                                    [optional]" name="pwhere" optional="True" type="text"/>
		<param label="--p-exclude-ids: --p-no-exclude-ids If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained.                        [default: False]" name="pexcludeids" selected="False" type="boolean"/>

		<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}: filtereddata.qza" name="ofiltereddata"/>
	</outputs>
	<help><![CDATA[
Filter features from sequences
##############################

Filter features from sequences based on a feature table or metadata. See
the filtering tutorial on https://docs.qiime2.org for additional details.
This method can filter based on ids in a table or a metadata file, but not
both (i.e., the table and metadata options are mutually exclusive).

Parameters
----------
data : FeatureData[Sequence]
    The sequences from which features should be filtered.
table : FeatureTable[Frequency], optional
    Table containing feature ids used for id-based filtering.
metadata : Metadata, optional
    Feature metadata used for id-based filtering, with `where` parameter
    when selecting features to retain, or with `exclude_ids` when selecting
    features to discard.
where : Str, optional
    SQLite WHERE clause specifying feature metadata criteria that must be
    met to be included in the filtered feature table. If not provided, all
    features in `metadata` that are also in the sequences will be retained.
exclude_ids : Bool, optional
    If true, the features selected by the `metadata` (with or without the
    `where` parameter) or `table` parameter will be excluded from the
    filtered sequences instead of being retained.

Returns
-------
filtered_data : FeatureData[Sequence]
    The resulting filtered sequences.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>