Mercurial > repos > q2d2 > qiime2__feature_classifier__blast
changeset 3:18cf1aa7f508 draft
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 21:05:17 +0000 |
parents | 778c23c7bcf3 |
children | 6f881a1c40be |
files | qiime2__feature_classifier__blast.xml |
diffstat | 1 files changed, 18 insertions(+), 12 deletions(-) [+] |
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--- a/qiime2__feature_classifier__blast.xml Thu Jun 08 19:43:47 2023 +0000 +++ b/qiime2__feature_classifier__blast.xml Thu Apr 25 21:05:17 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 blast" id="qiime2__feature_classifier__blast" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 feature-classifier blast" id="qiime2__feature_classifier__blast" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>BLAST+ local alignment search.</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 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."> @@ -27,13 +27,19 @@ </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> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <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="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="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."/>