diff qiime2/qiime_feature-classifier_classify-consensus-blast.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-classifier_classify-consensus-blast.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,140 @@
+<?xml version="1.0" ?>
+<tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast" version="2019.4">
+	<description> - BLAST+ consensus taxonomy classifier</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime feature-classifier classify-consensus-blast
+
+--i-query=$iquery
+--i-reference-reads=$ireferencereads
+
+#if str( $id_to_taxonomy_fp.selector ) == 'history'
+#set $tax = $id_to_taxonomy_fp.taxonomy_fp
+--i-reference-taxonomy '$tax'
+#else:
+#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
+--i-reference-taxonomy '$tax'
+#end if
+
+
+#if $pmaxaccepts:
+ --p-maxaccepts=$pmaxaccepts
+#end if
+
+#if $ppercidentity:
+ --p-perc-identity=$ppercidentity
+#end if
+
+#if $pquerycov:
+ --p-query-cov=$pquerycov
+#end if
+
+#if str($pstrand) != 'None':
+ --p-strand=$pstrand
+#end if
+
+#if $pevalue:
+ --p-evalue=$pevalue
+#end if
+
+#if $pminconsensus:
+ --p-min-consensus=$pminconsensus
+#end if
+
+#if str($punassignablelabel):
+ --p-unassignable-label="$punassignablelabel"
+#end if
+
+--o-classification=oclassification
+;
+cp oclassification.qza $oclassification
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically.      [required]" name="iquery" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences.                      [required]" name="ireferencereads" optional="False" type="data"/>
+
+		<conditional name="id_to_taxonomy_fp" optional="True">
+		   <param name="selector" type="select" label="Reference taxonomy to query">
+			  <option value="cached">Public databases</option>
+			  <option value="history">Databases from your history</option>
+		   </param>
+		   <when value="cached">
+			  <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
+				 <options from_data_table="qiime_taxonomy" />
+			  </param>
+		   </when>
+		   <when value="history">
+			  <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
+		   </when>
+		</conditional>
+
+		<param label="--p-maxaccepts: INTEGER  Maximum number of hits to keep for each query. Must Range(1, None)        be in range [1, infinity]. BLAST will choose the first N hits in the reference database that exceed perc-identity similarity to query.     [default: 10]" name="pmaxaccepts" optional="True" type="integer" min="1" value="10"/>
+		<param label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. Must be in range [0.0, 1.0].          [default: 0.8]" name="ppercidentity" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.8"/>
+		<param label="--p-query-cov: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. Must be in range [0.0, 1.0].                                 [default: 0.8]" name="pquerycov" optional="True" min="0" max="1" exclude_max="False" type="float" value="0.8"/>
+		<param label="--p-strand: " name="pstrand" optional="True" type="select">
+			<option selected="True" value="None">Selection is Optional</option>
+			<option value="both">both</option>
+			<option value="plus">plus</option>
+			<option value="minus">minus</option>
+		</param>
+		<param label="--p-evalue: NUMBER       BLAST expectation value (E) threshold for saving hits.                               [default: 0.001]" name="pevalue" optional="True" type="float" value="0.001"/>
+		<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'"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
+	</outputs>
+	<help><![CDATA[
+BLAST+ consensus taxonomy classifier
+####################################
+
+Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local
+alignment between query and reference_reads, then assigns consensus
+taxonomy to each query sequence from among maxaccepts hits, min_consensus
+of which share that taxonomic assignment. Note that maxaccepts selects the
+first N hits with > perc_identity similarity to query, not the top N
+matches. For top N hits, use classify-consensus-vsearch.
+
+Parameters
+----------
+query : FeatureData[Sequence]
+    Sequences to classify taxonomically.
+reference_reads : FeatureData[Sequence]
+    reference sequences.
+reference_taxonomy : FeatureData[Taxonomy]
+    reference taxonomy labels.
+maxaccepts : Int % Range(1, None), optional
+    Maximum number of hits to keep for each query. Must be in range [1,
+    infinity]. BLAST will choose the first N hits in the reference database
+    that exceed perc_identity similarity to query.
+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].
+query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
+    Reject match if query alignment coverage per high-scoring pair is
+    lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not
+    behave identically to the query_cov parameter used by classify-
+    consensus-vsearch. Must be in range [0.0, 1.0].
+strand : Str % Choices('both', 'plus', 'minus'), optional
+    Align against reference sequences in forward ("plus"), reverse
+    ("minus"), or both directions ("both").
+evalue : Float, optional
+    BLAST expectation value (E) threshold for saving hits.
+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].
+unassignable_label : Str, optional
+	\
+
+Returns
+-------
+classification : FeatureData[Taxonomy]
+    Taxonomy classifications of query sequences.
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>