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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_filter-samples.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,120 @@
+<?xml version="1.0" ?>
+<tool id="qiime_feature-table_filter-samples" name="qiime feature-table filter-samples" version="2019.4">
+	<description> - Filter samples from table</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime feature-table filter-samples
+
+--i-table=$itable
+
+
+#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 $pminfrequency:
+ --p-min-frequency=$pminfrequency
+#end if
+
+#if str($pmaxfrequency):
+ --p-max-frequency="$pmaxfrequency"
+#end if
+
+#if $pminfeatures:
+ --p-min-features=$pminfeatures
+#end if
+
+#if str($pmaxfeatures):
+ --p-max-features="$pmaxfeatures"
+#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-table=ofilteredtable
+;
+cp ofilteredtable.qza $ofilteredtable
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴] The feature table from which samples should be filtered.                                    [required]" name="itable" optional="False" type="data"/>
+		<param label="--p-min-frequency: INTEGER The minimum total frequency that a sample must have to be retained.                               [default: 0]" name="pminfrequency" optional="True" type="integer" value="0"/>
+		<param label="--p-max-frequency: INTEGER The maximum total frequency that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied).                                    [optional]" name="pmaxfrequency" optional="True" type="integer"/>
+		<param label="--p-min-features: INTEGER The minimum number of features that a sample must have to be retained.                            [default: 0]" name="pminfeatures" optional="True" type="integer" value="0"/>
+		<param label="--p-max-features: INTEGER The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied).                            [optional]" name="pmaxfeatures" optional="True" type="integer"/>
+		<param label="--p-where: TEXT       SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table 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 table 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}: filteredtable.qza" name="ofilteredtable"/>
+	</outputs>
+	<help><![CDATA[
+Filter samples from table
+#########################
+
+Filter samples from table based on frequency and/or metadata. Any features
+with a frequency of zero after sample filtering will also be removed. See
+the filtering tutorial on https://docs.qiime2.org for additional details.
+
+Parameters
+----------
+table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
+    The feature table from which samples should be filtered.
+min_frequency : Int, optional
+    The minimum total frequency that a sample must have to be retained.
+max_frequency : Int, optional
+    The maximum total frequency that a sample can have to be retained. If
+    no value is provided this will default to infinity (i.e., no maximum
+    frequency filter will be applied).
+min_features : Int, optional
+    The minimum number of features that a sample must have to be retained.
+max_features : Int, optional
+    The maximum number of features that a sample can have to be retained.
+    If no value is provided this will default to infinity (i.e., no maximum
+    feature filter will be applied).
+metadata : Metadata, optional
+    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 feature table. If not provided, all
+    samples in `metadata` that are also in the feature table will be
+    retained.
+exclude_ids : Bool, optional
+    If true, the samples selected by `metadata` or `where` parameters will
+    be excluded from the filtered table instead of being retained.
+
+Returns
+-------
+filtered_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
+    The resulting feature table filtered by sample.
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>