diff qiime2/qiime_diversity_filter-distance-matrix.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_filter-distance-matrix.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,92 @@
+<?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 $ofiltereddistancematrix
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix     Distance matrix to filter by sample.         [required]" name="idistancematrix" optional="False" type="data"/>
+		<param label="--p-where: TEXT       SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained.                     [optional]" name="pwhere" optional="True" type="text"/>
+		<param label="--p-exclude-ids: --p-no-exclude-ids If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained. [default: False]" name="pexcludeids" selected="False" type="boolean"/>
+
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+
+	</inputs>
+	<outputs>
+		<data format="qza" label="${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>