Mercurial > repos > q2d2 > qiime2__feature_classifier__classify_consensus_blast

changeset 3:f30561d08160 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:05:46 +0000
parents 8f8f6d3d2304
children 1ca4b5d6ea40
files qiime2__feature_classifier__classify_consensus_blast.xml
diffstat 1 files changed, 18 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__feature_classifier__classify_consensus_blast.xml	Thu Jun 08 19:43:26 2023 +0000
+++ b/qiime2__feature_classifier__classify_consensus_blast.xml	Thu Apr 25 21:05:46 2024 +0000
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 feature-classifier classify-consensus-blast" id="qiime2__feature_classifier__classify_consensus_blast" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 feature-classifier classify-consensus-blast" id="qiime2__feature_classifier__classify_consensus_blast" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>BLAST+ consensus taxonomy classifier</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version feature_classifier</version_command>
     <command detect_errors="exit_code">q2galaxy run feature_classifier classify_consensus_blast '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="query" type="data" format="qza" label="query: FeatureData[Sequence]" help="[required]  Query sequences.">
@@ -27,12 +27,6 @@
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
         </param>
-        <param name="reference_reads" type="data" format="qza" label="reference_reads: FeatureData[Sequence]" help="[required]  Reference sequences.">
-            <options options_filter_attribute="metadata.semantic_type">
-                <filter type="add_value" value="FeatureData[Sequence]"/>
-            </options>
-            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
-        </param>
         <param name="reference_taxonomy" type="data" format="qza" label="reference_taxonomy: FeatureData[Taxonomy]" help="[required]  reference taxonomy labels.">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureData[Taxonomy]"/>
@@ -40,6 +34,18 @@
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="blastdb" type="data" format="qza" optional="true" label="blastdb: BLASTDB" help="[optional]  BLAST indexed database. Incompatible with reference_reads.">
+                <options options_filter_attribute="metadata.semantic_type">
+                    <filter type="add_value" value="BLASTDB"/>
+                </options>
+                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['BLASTDB']</validator>
+            </param>
+            <param name="reference_reads" type="data" format="qza" optional="true" label="reference_reads: FeatureData[Sequence]" help="[optional]  Reference sequences. Incompatible with blastdb.">
+                <options options_filter_attribute="metadata.semantic_type">
+                    <filter type="add_value" value="FeatureData[Sequence]"/>
+                </options>
+                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
+            </param>
             <param name="maxaccepts" type="integer" min="1" value="10" label="maxaccepts: Int % Range(1, None)" help="[default: 10]  Maximum number of hits to keep for each query. BLAST will choose the first N hits in the reference database that exceed perc_identity similarity to query. NOTE: the database is not sorted by similarity to query, so these are the first N hits that pass the threshold, not necessarily the top N hits."/>
             <param name="perc_identity" type="float" min="0.0" max="1.0" value="0.8" label="perc_identity: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.8]  Reject match if percent identity to query is lower."/>
             <param name="query_cov" type="float" min="0.0" max="1.0" value="0.8" label="query_cov: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.8]  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."/>