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Changeset 0:4b35a77cde45 (2022-08-29)

Next changeset 1:931254bf17a4 (2023-01-13)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

added:
qiime2__phylogeny__iqtree.xml
test-data/.gitkeep

diff -r 000000000000 -r 4b35a77cde45 qiime2__phylogeny__iqtree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__phylogeny__iqtree.xml Mon Aug 29 20:18:24 2022 +0000

[

b'@@ -0,0 +1,380 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+\n+\n+<tool name="qiime2 phylogeny iqtree" id="qiime2__phylogeny__iqtree" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">\n+ <description>Construct a phylogenetic tree with IQ-TREE.</description>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/core:2022.8</container>\n+ </requirements>\n+ <version_command>q2galaxy version phylogeny</version_command>\n+ <command detect_errors="aggressive">q2galaxy run phylogeny iqtree \'$inputs\'</command>\n+ <configfiles>\n+ <inputs name="inputs" data_style="paths"/>\n+ </configfiles>\n+ <inputs>\n+ <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required] Aligned sequences to be used for phylogenetic reconstruction.">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="FeatureData[AlignedSequence]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'FeatureData[AlignedSequence]\']</validator>\n+ </param>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <param name="seed" type="integer" optional="true" label="seed: Int" help="[optional] Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details."/>\n+ <conditional name="__q2galaxy__GUI__conditional__n_cores__">\n+ <param name="__q2galaxy__GUI__select__" type="select" label="n_cores: Int % Range(1, None) | Str % Choices(\'auto\')" help="[default: 1] The number of cores to use for parallel processing. Use `auto` to let IQ-TREE automatically determine the optimal number of cores to use.">\n+ <option value="auto">auto (Str)</option>\n+ <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>\n+ </param>\n+ <when value="auto">\n+ <param name="n_cores" type="hidden" value="auto"/>\n+ </when>\n+ <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">\n+ <param name="n_cores" type="integer" min="1" value="1" label="n_cores: Int % Range(1, None)" help="[default: 1] The number of cores to use for parallel processing. Use `auto` to let IQ-TREE automatically determine the optimal number of cores to use."/>\n+ </when>\n+ </conditional>\n+ <param name="n_cores_max" type="integer" min="2" optional="true" label="n_cores_max: Int % Range(2, None)" help="[optional] Limits the maximum number of cores to be used when \'n_cores\' is set to \'auto\'."/>\n+ <param name="n_runs" type="integer" min="1" value="1" label="n_runs: Int % Range(1, None)" help="[default: 1] Number of indepedent runs. Multiple independent runs (e.g. 10) can outperform a single run in terms of likelihood maximisation."/>\n+ <param name="substitution_model" type="select" label="substitution_model: Str % Choices(\'JC\', \'JC+I\', \'JC+G\', \'JC+I+G\', \'JC+R2\', \'JC+R3\', \'JC+R4\', \'JC+R5\', \'JC+R6\', \'JC+R7\', \'JC+R8\', \'JC+R9\', \'JC+R10\', \'F81\', \'F81+I\', \'F81+G\', \'F81+I+G\', \'F81+R2\', \'F81+R3\', \'F81+R4\', \'F81+R5\', \'F81+R6\', \'F81+R7\', \'F81+R8\', \'F81+R9\', \'F81+R10\', \'K80\', \'K80+I\', \'K80+G\', \'K80+I+G\', \'K80+R2\', \'K80+R3\', \'K80+R4\', \'K80+R5\', \'K80+R6\', \'K80+R7\', \'K80+R8\', \'K80+R9\', \'K80+R10\', \'HKY\', \'HKY+I\', \'HKY+G\', \'HKY+I+G\', \'HKY+R2\', \'HKY+R3\', \'HKY+R4\', \'HKY+R5\', \'HKY+R6\', \'HKY+R7\', '..b' Int % Range(1, None)" help="[optional] Number of top initial trees. If not set, program defaults will be used. See IQ-TREE manual for details."/>\n+ <param name="n_best_retain_trees" type="integer" min="1" optional="true" label="n_best_retain_trees: Int % Range(1, None)" help="[optional] Number of best trees retained during search. If not set, program defaults will be used. See IQ-TREE manual for details."/>\n+ <param name="n_iter" type="integer" min="1" optional="true" label="n_iter: Int % Range(1, None)" help="[optional] Fix number of iterations to stop. If not set, program defaults will be used. See IQ-TREE manual for details."/>\n+ <param name="stop_iter" type="integer" min="1" optional="true" label="stop_iter: Int % Range(1, None)" help="[optional] Number of unsuccessful iterations to stop. If not set, program defaults will be used. See IQ-TREE manual for details."/>\n+ <param name="perturb_nni_strength" type="float" min="0.01" max="0.999999" optional="true" label="perturb_nni_strength: Float % Range(0.01, 1.0)" help="[optional] Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details."/>\n+ <param name="spr_radius" type="integer" min="1" optional="true" label="spr_radius: Int % Range(1, None)" help="[optional] Radius for parsimony SPR search. If not set, program defaults will be used. See IQ-TREE manual for details."/>\n+ <param name="allnni" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allnni: Bool" help="[default: No] Perform more thorough NNI search."/>\n+ <param name="fast" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="fast: Bool" help="[default: No] Fast search to resemble FastTree."/>\n+ <param name="alrt" type="integer" min="1000" optional="true" label="alrt: Int % Range(1000, None)" help="[optional] Single branch test method. Number of bootstrap replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes."/>\n+ <param name="abayes" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="abayes: Bool" help="[default: No] Single branch test method. Approximate Bayes test. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes."/>\n+ <param name="lbp" type="integer" min="1000" optional="true" label="lbp: Int % Range(1000, None)" help="[optional] Single branch test method. Number of bootstrap replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes."/>\n+ <param name="safe" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="safe: Bool" help="[default: No] Safe likelihood kernel to avoid numerical underflow."/>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>\n+ </outputs>\n+ <tests/>\n+ <help>\n+QIIME 2: phylogeny iqtree\n+=========================\n+Construct a phylogenetic tree with IQ-TREE.\n+\n+\n+Outputs:\n+--------\n+:tree.qza: The resulting phylogenetic tree.\n+\n+| \n+\n+Description:\n+------------\n+Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with automatic model selection.\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="doi">10.1093/molbev/msaa015</citation>\n+ <citation type="doi">10.1038/nmeth.4285</citation>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n'