Galaxy |

Changeset 0:6506a4307430 (2022-08-29)

Next changeset 1:9f7b98404a1f (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__align_to_tree_mafft_iqtree.xml
test-data/.gitkeep

diff -r 000000000000 -r 6506a4307430 qiime2__phylogeny__align_to_tree_mafft_iqtree.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml Mon Aug 29 20:18:00 2022 +0000

[

b'@@ -0,0 +1,375 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+\n+\n+<tool name="qiime2 phylogeny align-to-tree-mafft-iqtree" id="qiime2__phylogeny__align_to_tree_mafft_iqtree" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">\n+ <description>Build a phylogenetic tree using iqtree and mafft alignment.</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 align_to_tree_mafft_iqtree \'$inputs\'</command>\n+ <configfiles>\n+ <inputs name="inputs" data_style="paths"/>\n+ </configfiles>\n+ <inputs>\n+ <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] The sequences to be used for creating a iqtree based rooted phylogenetic tree.">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="FeatureData[Sequence]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'FeatureData[Sequence]\']</validator>\n+ </param>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <conditional name="__q2galaxy__GUI__conditional__n_threads__">\n+ <param name="__q2galaxy__GUI__select__" type="select" label="n_threads: Int % Range(1, None) | Str % Choices(\'auto\')" help="[default: 1] The number of threads. (Use 0 to automatically use all available cores This value is used when aligning the sequences and creating the tree with iqtree.">\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_threads" type="hidden" value="auto"/>\n+ </when>\n+ <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">\n+ <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1] The number of threads. (Use 0 to automatically use all available cores This value is used when aligning the sequences and creating the tree with iqtree."/>\n+ </when>\n+ </conditional>\n+ <param name="mask_max_gap_frequency" type="float" min="0" max="1" value="1.0" label="mask_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. This value is used when masking the aligned sequences."/>\n+ <param name="mask_min_conservation" type="float" min="0" max="1" value="0.4" label="mask_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. This value is used when masking the aligned sequences."/>'..b'tion>\n+ <option value="GTR">GTR</option>\n+ <option value="GTR+I">GTR+I</option>\n+ <option value="GTR+G">GTR+G</option>\n+ <option value="GTR+I+G">GTR+I+G</option>\n+ <option value="GTR+R2">GTR+R2</option>\n+ <option value="GTR+R3">GTR+R3</option>\n+ <option value="GTR+R4">GTR+R4</option>\n+ <option value="GTR+R5">GTR+R5</option>\n+ <option value="GTR+R6">GTR+R6</option>\n+ <option value="GTR+R7">GTR+R7</option>\n+ <option value="GTR+R8">GTR+R8</option>\n+ <option value="GTR+R9">GTR+R9</option>\n+ <option value="GTR+R10">GTR+R10</option>\n+ <option value="MFP" selected="true">MFP</option>\n+ <option value="TEST">TEST</option>\n+ </param>\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."/>\n+ <param name="seed" type="integer" optional="true" label="seed: Int" help="[optional] Random number seed for the iqtree parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."/>\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+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="alignment" format="qza" label="${tool.name} on ${on_string}: alignment.qza" from_work_dir="alignment.qza"/>\n+ <data name="masked_alignment" format="qza" label="${tool.name} on ${on_string}: masked_alignment.qza" from_work_dir="masked_alignment.qza"/>\n+ <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>\n+ <data name="rooted_tree" format="qza" label="${tool.name} on ${on_string}: rooted_tree.qza" from_work_dir="rooted_tree.qza"/>\n+ </outputs>\n+ <tests/>\n+ <help>\n+QIIME 2: phylogeny align-to-tree-mafft-iqtree\n+=============================================\n+Build a phylogenetic tree using iqtree and mafft alignment.\n+\n+\n+Outputs:\n+--------\n+:alignment.qza: The aligned sequences.\n+:masked_alignment.qza: The masked alignment.\n+:tree.qza: The unrooted phylogenetic tree.\n+:rooted_tree.qza: The rooted phylogenetic tree.\n+\n+| \n+\n+Description:\n+------------\n+This pipeline will start by creating a sequence alignment using MAFFT, after which any alignment columns that are phylogenetically uninformative or ambiguously aligned will be removed (masked). The resulting masked alignment will be used to infer a phylogenetic tree using IQ-TREE. By default the best fit substitution model will be determined by ModelFinder prior to phylogenetic inference. The resulting tree will be subsequently rooted at its midpoint. Output files from each step of the pipeline will be saved. This includes both the unmasked and masked MAFFT alignment from q2-alignment methods, and both the rooted and unrooted phylogenies from q2-phylogeny methods.\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n'