annotate qiime2/qiime_diversity_filter-distance-matrix.xml @ 8:d66c7509e8f9 draft

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<?xml version="1.0" ?>
<tool id="qiime_diversity_filter-distance-matrix" name="qiime diversity filter-distance-matrix" version="2019.4">
	<description> - Filter samples from a distance matrix.</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime diversity filter-distance-matrix

--i-distance-matrix=$idistancematrix


#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 '__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-distance-matrix=ofiltereddistancematrix
;
cp ofiltereddistancematrix.qza $ofiltereddistancematrix
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix     Distance matrix to filter by sample.         [required]" name="idistancematrix" optional="False" type="data"/>
		<param label="--p-where: TEXT       SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained.                     [optional]" name="pwhere" optional="True" type="text"/>
		<param label="--p-exclude-ids: --p-no-exclude-ids If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean"/>

		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
			<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}: filtereddistancematrix.qza" name="ofiltereddistancematrix"/>
	</outputs>
	<help><![CDATA[
Filter samples from a distance matrix.
######################################

Filter samples from a distance matrix, retaining only the samples matching
search criteria specified by `metadata` and `where` parameters (or
retaining only the samples not matching that criteria, if `exclude_ids` is
True). See the filtering tutorial on https://docs.qiime2.org for additional
details.

Parameters
----------
distance_matrix : DistanceMatrix
    Distance matrix to filter by sample.
metadata : Metadata
    Sample metadata used with `where` parameter when selecting samples to
    retain, or with `exclude_ids` when selecting samples to discard.
where : Str, optional
    SQLite WHERE clause specifying sample metadata criteria that must be
    met to be included in the filtered distance matrix. If not provided,
    all samples in `metadata` that are also in the input distance matrix
    will be retained.
exclude_ids : Bool, optional
    If `True`, the samples selected by `metadata` or `where` parameters
    will be excluded from the filtered distance matrix instead of being
    retained.

Returns
-------
filtered_distance_matrix : DistanceMatrix
    Distance matrix filtered to include samples matching search criteria
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>