New tool: PhyloPhlAn an integrated pipeline for phylogenetic profiling of genomes and metagenomes#7067
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neo417 wants to merge 15 commits intogalaxyproject:mainfrom
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New tool: PhyloPhlAn an integrated pipeline for phylogenetic profiling of genomes and metagenomes#7067neo417 wants to merge 15 commits intogalaxyproject:mainfrom
neo417 wants to merge 15 commits intogalaxyproject:mainfrom
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…filing of genomes and metagenomes. PhyloPhlAn GitHub: https://github.com/biobakery/phylophlan The tool suite consists of multiple scripts which need to be wrapped into tools and data managers, but this branch is only concerned with creating the tool wrappers. As of this commit only phylophlan.xml is largely complete. This is the main script to run the Concatenation and Gene-trees pipelines, and allows the user to configure which external tools they want to use at every analysis step. - Support for some preconfigured external tools is missing (Opal, UPP and astrid). - Using aligned markers from StrainPhlAn (--strainphlan) is not supported. - Code and .loc files to access cached datasets are missing. phylophlan_assign_sgbs and phylophlan_draw_metagenomic are used to report and visualize the closest species-level genome bins, for each bin from a metagenomic assembly analysis. My progress on them has recently stalled, because the scripts rely entirely on the presence of a cached database, which I did not implement like above. Besides that they are missing an expanded help section, and the current release of the assign_sgbs script has a bug limiting some of the functionality (pairwise mash distances of the input). phylophlan_strain_finder would be a tool to perform analysis on trees and mutation rate tables build with phylophlan, but I have not wrapped it (yet?). The test data have been created by cutting down example data from the tutorials on the PhyloPhlAn github.
Cached databases use the unique ID as the database name. This is used to enable phylophlan to override some parameters for the PhyloPhlAn and AMPHORA2 databases.
If this works now on the online checks I don't understand why it worked on my planemo instance the entire time.
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@Minamehr would you like to review this in more detail? |
Minamehr
reviewed
Jul 25, 2025
Co-authored-by: Mina Hojat Ansari <73378149+Minamehr@users.noreply.github.com> Also remove spaces in empty lines in python code.
… would support out of the box.
SaimMomin12
reviewed
Aug 1, 2025
| <macros> | ||
| <token name="@TOOL_VERSION@">3.1.1</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">23.0</token> |
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| <token name="@PROFILE@">23.0</token> | |
| <token name="@PROFILE@">24.2</token> |
| <xml name="requirements"> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">phylophlan</requirement> | ||
| <yield/> |
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| <yield/> |
| <!-- PhyloPhlAn input blocks --> | ||
| <xml name="config_select_software"> | ||
| <conditional name="db"> | ||
| <param name="type" type="select" argument="-d / -t" label="Database marker type"> |
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is it possible to stick to one argument either -d or -t?
| <xml name="citations"> | ||
| <citations> | ||
| <citation type="doi">10.1038/s41467-020-16366-7</citation> | ||
| <yield/> |
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| <yield/> |
| @@ -0,0 +1,604 @@ | |||
| <tool id="phylophlan" name="PhyloPhlAn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |||
| <description> | |||
| microbial genome characterization and phylogenetic analysis | |||
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| microbial genome characterization and phylogenetic analysis | |
| Microbial genome characterization and phylogenetic analysis |
| <option value="muscle">muscle</option> | ||
| <!-- Todo: Find packages for the tools opal and upp and add options for them here. --> | ||
| </param> | ||
| <yield/> |
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| <yield/> |
| <command detect_errors="exit_code"><
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FOR CONTRIBUTOR:
As suggested by @SaimMomin12, I am also moving this pull request here from bgruening/galaxytools#1639.
PhyloPhlAn comes with a few scripts for downloading reference data, some of which might be more appropriate as data managers. The indices certainly need to be cached. One script (phylophlan_strain_finder) for downstream analysis of trees and mutation rates build with phylophlan still needs to be wrapped as well. Sadly, I don't have the time to work on that at the moment.
Would it be useful to publish what is ready now and add the remaining tools and data managers later?