diff qiime2/qiime_feature-table_filter-seqs.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_filter-seqs.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,97 @@
+<?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>