diff qiime2-2020.8/qiime_feature-classifier_classify-consensus-blast.xml @ 20:d93d8888f0b0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_feature-classifier_classify-consensus-blast.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,119 @@
+<?xml version="1.0" ?>
+<tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast"
+      version="2020.8">
+  <description>BLAST+ consensus taxonomy classifier</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime feature-classifier classify-consensus-blast
+
+--i-query=$iquery
+
+--i-reference-reads=$ireferencereads
+
+--i-reference-taxonomy=$ireferencetaxonomy
+
+--p-maxaccepts=$pmaxaccepts
+
+--p-perc-identity=$ppercidentity
+
+--p-query-cov=$pquerycov
+
+#if str($pstrand) != 'None':
+--p-strand=$pstrand
+#end if
+
+--p-evalue=$pevalue
+
+--p-min-consensus=$pminconsensus
+
+#if str($punassignablelabel):
+  --p-unassignable-label=$punassignablelabel
+#end if
+--o-classification=oclassification
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+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" />
+    <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels.                [required]" name="ireferencetaxonomy" optional="False" type="data" />
+    <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]" min="1" name="pmaxaccepts" optional="True" type="integer" value="10" />
+    <param exclude_max="False" 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]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.8" />
+    <param exclude_max="False" 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]" max="1.0" min="0.0" name="pquerycov" optional="True" 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 exclude_max="False" exclude_min="True" 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]" max="1.0" min="0.5" name="pminconsensus" optional="True" type="float" value="0.51" />
+    <param label="--p-unassignable-label: TEXT [default: \'Unassigned\']" name="punassignablelabel" optional="False" type="text" value="\'Unassigned\'" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </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>
\ No newline at end of file