# HG changeset patch # User q2d2 # Date 1661804280 0 # Node ID 6506a43074307bc8f3b35727682adf840c60c70c planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 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 @@ -0,0 +1,375 @@ + + + + + Build a phylogenetic tree using iqtree and mafft alignment. + + quay.io/qiime2/core:2022.8 + + q2galaxy version phylogeny + q2galaxy run phylogeny align_to_tree_mafft_iqtree '$inputs' + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]'] + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + + + + + + +QIIME 2: phylogeny align-to-tree-mafft-iqtree +============================================= +Build a phylogenetic tree using iqtree and mafft alignment. + + +Outputs: +-------- +:alignment.qza: The aligned sequences. +:masked_alignment.qza: The masked alignment. +:tree.qza: The unrooted phylogenetic tree. +:rooted_tree.qza: The rooted phylogenetic tree. + +| + +Description: +------------ +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. + + +| + + + + 10.1038/s41587-019-0209-9 + + diff -r 000000000000 -r 6506a4307430 test-data/.gitkeep