Mercurial > repos > q2d2 > qiime2__diversity_lib__unweighted_unifrac
changeset 3:60cbf3e37ee1 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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--- a/qiime2__diversity_lib__unweighted_unifrac.xml Thu Jun 08 19:40:07 2023 +0000 +++ b/qiime2__diversity_lib__unweighted_unifrac.xml Thu Apr 25 21:04:04 2024 +0000 @@ -1,24 +1,24 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2023, QIIME 2 development team. +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: 2023.5.0) + q2galaxy (version: 2024.2.1) for: - qiime2 (version: 2023.5.1) + qiime2 (version: 2024.2.0) --> -<tool name="qiime2 diversity-lib unweighted-unifrac" id="qiime2__diversity_lib__unweighted_unifrac" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 diversity-lib unweighted-unifrac" id="qiime2__diversity_lib__unweighted_unifrac" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>Unweighted Unifrac</description> <requirements> - <container type="docker">quay.io/qiime2/core:2023.5</container> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> </requirements> <version_command>q2galaxy version diversity_lib</version_command> <command detect_errors="exit_code">q2galaxy run diversity_lib unweighted_unifrac '$inputs'</command> <configfiles> - <inputs name="inputs" data_style="paths"/> + <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples for which Unweighted Unifrac should be computed."> @@ -36,18 +36,6 @@ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator> </param> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> - <conditional name="__q2galaxy__GUI__conditional__threads__"> - <param name="__q2galaxy__GUI__select__" type="select" label="threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."> - <option value="auto">auto (Str)</option> - <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option> - </param> - <when value="auto"> - <param name="threads" type="hidden" value="auto"/> - </when> - <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> - <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1] The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."/> - </when> - </conditional> <param name="bypass_tips" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bypass_tips: Bool" help="[default: No] In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs"/> </section> </inputs> @@ -69,10 +57,6 @@ <test> <param name="table" value="unweighted_unifrac.test1.feature-table.qza" ftype="qza"/> <param name="phylogeny" value="unweighted_unifrac.test1.phylogeny.qza" ftype="qza"/> - <conditional name="__q2galaxy__GUI__conditional__threads__"> - <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/> - <param name="threads" value="1"/> - </conditional> <output name="distance_matrix" ftype="qza"> <assert_contents> <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> @@ -84,10 +68,6 @@ <test> <param name="table" value="unweighted_unifrac.test2.feature-table.qza" ftype="qza"/> <param name="phylogeny" value="unweighted_unifrac.test2.phylogeny.qza" ftype="qza"/> - <conditional name="__q2galaxy__GUI__conditional__threads__"> - <param name="__q2galaxy__GUI__select__" value="auto"/> - <param name="threads" value="auto"/> - </conditional> <output name="distance_matrix" ftype="qza"> <assert_contents> <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> @@ -99,10 +79,6 @@ <test> <param name="table" value="unweighted_unifrac.test3.feature-table.qza" ftype="qza"/> <param name="phylogeny" value="unweighted_unifrac.test3.phylogeny.qza" ftype="qza"/> - <conditional name="__q2galaxy__GUI__conditional__threads__"> - <param name="__q2galaxy__GUI__select__" value="auto"/> - <param name="threads" value="auto"/> - </conditional> <param name="bypass_tips" value="__q2galaxy__::literal::True"/> <output name="distance_matrix" ftype="qza"> <assert_contents> @@ -156,10 +132,6 @@ Using the ``qiime2 diversity-lib unweighted-unifrac`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Set *"phylogeny"* to ``#: phylogeny.qza`` - #. Expand the ``additional options`` section - - - Leave *"threads"* as its default value of ``1`` - #. Press the ``Execute`` button. Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: @@ -179,10 +151,6 @@ Using the ``qiime2 diversity-lib unweighted-unifrac`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Set *"phylogeny"* to ``#: phylogeny.qza`` - #. Expand the ``additional options`` section - - - Set *"threads"* to ``auto`` - #. Press the ``Execute`` button. Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: @@ -205,8 +173,7 @@ #. Set *"phylogeny"* to ``#: phylogeny.qza`` #. Expand the ``additional options`` section - #. Set *"threads"* to ``auto`` - #. Set *"bypass_tips"* to ``Yes`` + - Set *"bypass_tips"* to ``Yes`` #. Press the ``Execute`` button.