view qiime2__feature_classifier__blast.xml @ 3:18cf1aa7f508 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

<?xml version='1.0' encoding='utf-8'?>
<!--
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: 2024.2.1)
for:
    qiime2 (version: 2024.2.0)
-->
<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/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="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="query" type="data" format="qza" label="query: FeatureData[Sequence]" help="[required]  Query 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."/>
            <param name="strand" type="select" label="strand: Str % Choices('both', 'plus', 'minus')" display="radio">
                <option value="both" selected="true">both</option>
                <option value="plus">plus</option>
                <option value="minus">minus</option>
            </param>
            <param name="evalue" type="float" value="0.001" label="evalue: Float" help="[default: 0.001]  BLAST expectation value (E) threshold for saving hits."/>
            <param name="output_no_hits" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="output_no_hits: Bool" help="[default: Yes]  Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. Set to FALSE to mirror default BLAST search."/>
        </section>
    </inputs>
    <outputs>
        <data name="search_results" format="qza" label="${tool.name} on ${on_string}: search_results.qza" from_work_dir="search_results.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: feature-classifier blast
=================================
BLAST+ local alignment search.


Outputs:
--------
:search_results.qza: Top hits for each query.

|  

Description:
------------
Search for top hits in a reference database via local alignment between the query sequences and reference database sequences using BLAST+. Returns a report of the top M hits for each query (where M=maxaccepts).


|  

</help>
    <citations>
        <citation type="doi">10.1186/1471-2105-10-421</citation>
        <citation type="doi">10.1186/s40168-018-0470-z</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>