| Next changeset 1:58797be8efd4 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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added:
qiime2__alignment__mask.xml test-data/.gitkeep |
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| diff -r 000000000000 -r 610253dfe672 qiime2__alignment__mask.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__alignment__mask.xml Mon Aug 29 19:19:18 2022 +0000 |
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| @@ -0,0 +1,73 @@ +<?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 alignment mask" id="qiime2__alignment__mask" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Positional conservation and gap filtering.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version alignment</version_command> + <command detect_errors="aggressive">q2galaxy run alignment mask '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required] The alignment to be masked."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[AlignedSequence]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="max_gap_frequency" type="float" min="0" max="1" value="1.0" label="max_gap_frequency: Float % Range(0, 1, inclusive_end=True)" help="[default: 1.0] The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency."/> + <param name="min_conservation" type="float" min="0" max="1" value="0.4" label="min_conservation: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.4] The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences."/> + </section> + </inputs> + <outputs> + <data name="masked_alignment" format="qza" label="${tool.name} on ${on_string}: masked_alignment.qza" from_work_dir="masked_alignment.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: alignment mask +======================= +Positional conservation and gap filtering. + + +Outputs: +-------- +:masked_alignment.qza: The masked alignment. + +| + +Description: +------------ +Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991). + + +| + +</help> + <citations> + <citation type="bibtex">@incollection{cite1, + address = {New York}, + author = {Lane, DJ}, + booktitle = {Nucleic Acid Techniques in Bacterial Systematics}, + editor = {Stackebrandt, E and Goodfellow, M}, + pages = {115--175}, + publisher = {John Wiley and Sons}, + title = {16S/23S rRNA sequencing}, + year = {1991} +} +</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool> |