| Next changeset 1:f697a0b6a702 (2023-01-13) |
|
Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
|
added:
qiime2__quality_control__exclude_seqs.xml test-data/.gitkeep |
| b |
| diff -r 000000000000 -r 7e3db22e1eaf qiime2__quality_control__exclude_seqs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__quality_control__exclude_seqs.xml Mon Aug 29 20:20:21 2022 +0000 |
| [ |
| @@ -0,0 +1,82 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2022, 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: 2022.8.1) +for: + qiime2 (version: 2022.8.1) +--> +<tool name="qiime2 quality-control exclude-seqs" id="qiime2__quality_control__exclude_seqs" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Exclude sequences by alignment</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version quality_control</version_command> + <command detect_errors="aggressive">q2galaxy run quality_control exclude_seqs '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="query_sequences" type="data" format="qza" label="query_sequences: FeatureData[Sequence]" help="[required] Sequences to test for exclusion"> + <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_sequences" type="data" format="qza" label="reference_sequences: FeatureData[Sequence]" help="[required] Reference sequences to align against feature 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="method" type="select" label="method: Str % Choices('blast', 'blastn-short')¹ | Str % Choices('vsearch')²" help="[default: 'blast'] Alignment method to use for matching feature sequences against reference sequences"> + <option value="blast" selected="true">blast (Str)</option> + <option value="blastn-short">blastn-short (Str)</option> + <option value="vsearch">vsearch (Str)</option> + </param> + <param name="perc_identity" type="float" min="0.0" max="1.0" value="0.97" label="perc_identity: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.97] Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0]"/> + <param name="evalue" type="float" optional="true" label="evalue: Float" help="[optional] BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default."/> + <param name="perc_query_aligned" type="float" value="0.97" label="perc_query_aligned: Float" help="[default: 0.97] Percent of query sequence that must align to reference in order to be accepted as a hit."/> + <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1] Number of jobs to execute. Only applies to vsearch method."/> + <param name="left_justify" type="select" label="left_justify: Bool % Choices(False)¹ | Bool²" help="[default: No] Reject match if the pairwise alignment begins with gaps"> + <option value="__q2galaxy__::literal::False" selected="true">No (Bool)</option> + <option value="__q2galaxy__::literal::True">Yes (Bool)</option> + </param> + </section> + </inputs> + <outputs> + <data name="sequence_hits" format="qza" label="${tool.name} on ${on_string}: sequence_hits.qza" from_work_dir="sequence_hits.qza"/> + <data name="sequence_misses" format="qza" label="${tool.name} on ${on_string}: sequence_misses.qza" from_work_dir="sequence_misses.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: quality-control exclude-seqs +===================================== +Exclude sequences by alignment + + +Outputs: +-------- +:sequence_hits.qza: Subset of feature sequences that align to reference sequences +:sequence_misses.qza: Subset of feature sequences that do not align to reference sequences + +| + +Description: +------------ +This method aligns feature sequences to a set of reference sequences to identify sequences that hit/miss the reference within a specified perc_identity, evalue, and perc_query_aligned. This method could be used to define a positive filter, e.g., extract only feature sequences that align to a certain clade of bacteria; or to define a negative filter, e.g., identify sequences that align to contaminant or human DNA sequences that should be excluded from subsequent analyses. Note that filtering is performed based on the perc_identity, perc_query_aligned, and evalue thresholds (the latter only if method==BLAST and an evalue is set). Set perc_identity==0 and/or perc_query_aligned==0 to disable these filtering thresholds as necessary. + + +| + +</help> + <citations> + <citation type="doi">10.1186/1471-2105-10-421</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool> |