Mercurial > repos > q2d2 > qiime2__rescript__filter_seqs_length
changeset 0:8c16765c46bb draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author | q2d2 |
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date | Thu, 25 Apr 2024 21:19:49 +0000 |
parents | |
children | |
files | qiime2__rescript__filter_seqs_length.xml test-data/.gitkeep |
diffstat | 1 files changed, 67 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__rescript__filter_seqs_length.xml Thu Apr 25 21:19:49 2024 +0000 @@ -0,0 +1,67 @@ +<?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 rescript filter-seqs-length" id="qiime2__rescript__filter_seqs_length" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> + <description>Filter sequences by length.</description> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> + </requirements> + <version_command>q2galaxy version rescript</version_command> + <command detect_errors="exit_code">q2galaxy run rescript filter_seqs_length '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] Sequences to be filtered by length."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[Sequence]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="global_min" type="integer" min="1" optional="true" label="global_min: Int % Range(1, None)" help="[optional] The minimum length threshold for filtering all sequences. Any sequence shorter than this length will be removed."/> + <param name="global_max" type="integer" min="1" optional="true" label="global_max: Int % Range(1, None)" help="[optional] The maximum length threshold for filtering all sequences. Any sequence longer than this length will be removed."/> + <param name="threads" type="integer" min="1" max="255" value="1" label="threads: Int % Range(1, 256)" help="[default: 1] Number of computation threads to use (1 to 256). The number of threads should be lesser or equal to the number of available CPU cores."/> + </section> + </inputs> + <outputs> + <data name="filtered_seqs" format="qza" label="${tool.name} on ${on_string}: filtered_seqs.qza" from_work_dir="filtered_seqs.qza"/> + <data name="discarded_seqs" format="qza" label="${tool.name} on ${on_string}: discarded_seqs.qza" from_work_dir="discarded_seqs.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: rescript filter-seqs-length +==================================== +Filter sequences by length. + + +Outputs: +-------- +:filtered_seqs.qza: Sequences that pass the filtering thresholds. +:discarded_seqs.qza: Sequences that fall outside the filtering thresholds. + +| + +Description: +------------ +Filter sequences by length with VSEARCH. For a combination of global and conditional taxonomic filtering, see filter_seqs_length_by_taxon. + + +| + +</help> + <citations> + <citation type="doi">10.7717/peerj.2584</citation> + <citation type="doi">10.1371/journal.pcbi.1009581</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>