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comparison qiime2__feature_classifier__blast.xml @ 3:18cf1aa7f508 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 21:05:17 +0000
parents 778c23c7bcf3
children 6f881a1c40be
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2:778c23c7bcf3 3:18cf1aa7f508
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2023, QIIME 2 development team. 3 Copyright (c) 2024, QIIME 2 development team.
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2023.5.0) 9 q2galaxy (version: 2024.2.1)
10 for: 10 for:
11 qiime2 (version: 2023.5.1) 11 qiime2 (version: 2024.2.0)
12 --> 12 -->
13 <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"> 13 <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">
14 <description>BLAST+ local alignment search.</description> 14 <description>BLAST+ local alignment search.</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2023.5</container> 16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version feature_classifier</version_command> 18 <version_command>q2galaxy version feature_classifier</version_command>
19 <command detect_errors="exit_code">q2galaxy run feature_classifier blast '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run feature_classifier blast '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 23 <inputs>
24 <param name="query" type="data" format="qza" label="query: FeatureData[Sequence]" help="[required] Query sequences."> 24 <param name="query" type="data" format="qza" label="query: FeatureData[Sequence]" help="[required] Query sequences.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureData[Sequence]"/> 26 <filter type="add_value" value="FeatureData[Sequence]"/>
27 </options> 27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> 28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
29 </param> 29 </param>
30 <param name="reference_reads" type="data" format="qza" label="reference_reads: FeatureData[Sequence]" help="[required] Reference sequences.">
31 <options options_filter_attribute="metadata.semantic_type">
32 <filter type="add_value" value="FeatureData[Sequence]"/>
33 </options>
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
35 </param>
36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
31 <param name="reference_reads" type="data" format="qza" optional="true" label="reference_reads: FeatureData[Sequence]" help="[optional] Reference sequences. Incompatible with blastdb.">
32 <options options_filter_attribute="metadata.semantic_type">
33 <filter type="add_value" value="FeatureData[Sequence]"/>
34 </options>
35 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
36 </param>
37 <param name="blastdb" type="data" format="qza" optional="true" label="blastdb: BLASTDB" help="[optional] BLAST indexed database. Incompatible with reference_reads.">
38 <options options_filter_attribute="metadata.semantic_type">
39 <filter type="add_value" value="BLASTDB"/>
40 </options>
41 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['BLASTDB']</validator>
42 </param>
37 <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."/> 43 <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."/>
38 <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."/> 44 <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."/>
39 <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."/> 45 <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."/>
40 <param name="strand" type="select" label="strand: Str % Choices('both', 'plus', 'minus')" display="radio"> 46 <param name="strand" type="select" label="strand: Str % Choices('both', 'plus', 'minus')" display="radio">
41 <option value="both" selected="true">both</option> 47 <option value="both" selected="true">both</option>