diff qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml @ 9:f190567fe3f6 draft

Uploaded

--- a/qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml	Tue Aug 13 07:57:53 2019 -0400
+++ b/qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml	Wed Aug 14 15:12:48 2019 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0" ?>
-<tool id="qiime_feature-classifier_classify-consensus-vsearch" name="qiime feature-classifier classify-consensus-vsearch" version="2019.4">
+<tool id="qiime_feature-classifier_classify-consensus-vsearch" name="qiime feature-classifier classify-consensus-vsearch" version="2019.7">
 	<description> - VSEARCH consensus taxonomy classifier</description>
 	<requirements>
-		<requirement type="package" version="2019.4">qiime2</requirement>
+		<requirement type="package" version="2019.7">qiime2</requirement>
 	</requirements>
 	<command><![CDATA[
 qiime feature-classifier classify-consensus-vsearch
@@ -20,6 +20,16 @@
 #end if
 
 
+#if $psearchexact:
+  --p-search-exact
+#end if
+
+
+#if $ptophitsonly:
+  --p-top-hits-only
+#end if
+
+
 
 #if str($pmaxaccepts):
  --p-maxaccepts=$pmaxaccepts
@@ -63,6 +73,7 @@
 #end if
 
 --o-classification=oclassification
+
 ;
 cp oclassification.qza $oclassification
 	]]></command>
@@ -95,13 +106,17 @@
 		</param>
 		<param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True)   Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0].                    [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/>
 		<param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
+
+
+		<param label="--p-search-exact:  Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity and query-cov settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported.       [default: False]" name="psearchexact" selected="False" type="boolean"/>
+		<param label="--p-top-hits-only:  Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1.                    [default: False]" name="ptophitsonly" selected="False" type="boolean"/>
+
 	</inputs>
 	<outputs>
 		<data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
 	</outputs>
 	<help><![CDATA[
-VSEARCH consensus taxonomy classifier
-#####################################
+VSEARCH-based consensus taxonomy classifier
 
 Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
 alignment between query and reference_reads, then assigns consensus
@@ -118,23 +133,34 @@
     reference sequences.
 reference_taxonomy : FeatureData[Taxonomy]
     reference taxonomy labels.
-maxaccepts : Int % Range(0, None), optional
-    Maximum number of hits to keep for each query. Set to 0 to keep all
-    hits > perc_identity similarity. Must be in range [0, infinity].
+maxaccepts : Int % Range(1, None) | Str % Choices('all'), optional
+    Maximum number of hits to keep for each query. Set to "all" to keep all
+    hits > perc_identity similarity.
 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
-    Reject match if percent identity to query is lower. Must be in range
-    [0.0, 1.0].
+    Reject match if percent identity to query is lower.
 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
     Reject match if query alignment coverage per high-scoring pair is
-    lower. Must be in range [0.0, 1.0].
+    lower.
 strand : Str % Choices('both', 'plus'), optional
     Align against reference sequences in forward ("plus") or both
     directions ("both").
 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
     Minimum fraction of assignments must match top hit to be accepted as
-    consensus assignment. Must be in range (0.5, 1.0].
+    consensus assignment.
 unassignable_label : Str, optional
-	\
+search_exact : Bool, optional
+    Search for exact full-length matches to the query sequences. Only 100%
+    exact matches are reported and this command is much faster than the
+    default. If True, the perc_identity and query_cov settings are ignored.
+    Note: query and reference reads must be trimmed to the exact same DNA
+    locus (e.g., primer site) because only exact matches will be reported.
+top_hits_only : Bool, optional
+    Only the top hits between the query and reference sequence sets are
+    reported. For each query, the top hit is the one presenting the highest
+    percentage of identity. Multiple equally scored top hits will be used
+    for consensus taxonomic assignment if maxaccepts is greater than 1.
+threads : Int % Range(1, None), optional
+    Number of threads to use for job parallelization.
 
 Returns
 -------