New tool addition: amas tool #7443
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| categories: | ||
| - Phylogenetics | ||
| - Sequence Analysis | ||
| - Statistics | ||
| description: AMAS high-throughput alignment manipulation and summaries for phylogenomics | ||
| homepage_url: https://github.com/marekborowiec/AMAS | ||
| long_description: Handle expansive phylogenomic data sets by concatenating, removing, | ||
| replicating, splitting, and summarising large nucleotide or amino acid alignments. | ||
| name: amas | ||
| owner: iuc | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas | ||
| auto_tool_repositories: | ||
| name_template: "{{ tool_id }}" | ||
| description_template: "Wrapper for amas functions: {{ tool_name }}." | ||
| suite: | ||
| name: "suite_amas" | ||
| description: "A suite of tools that brings the amas project into Galaxy." | ||
| long_description: Handle expansive phylogenomic data sets by concatenating, removing, | ||
| replicating, splitting, and summarising large nucleotide or amino acid alignments. |
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| <tool id="amas_concat" name="AMAS concat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||||
| <description>concatenate multiple alignments</description> | ||||
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| <macros> | ||||
| <import>macros.xml</import> | ||||
| </macros> | ||||
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| <xrefs> | ||||
| <xref type="bio.tools">amas</xref> | ||||
| </xrefs> | ||||
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| <expand macro="requirements" /> | ||||
| <expand macro="version_command" /> | ||||
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| <command detect_errors="exit_code"><![CDATA[ | ||||
| #import re | ||||
| set -eu; | ||||
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| @SYMLINK_INPUTS@ | ||||
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| python -m amas.AMAS | ||||
| concat | ||||
| --concat-part partitions.txt | ||||
| --concat-out concatenated.out | ||||
| --part-format $part_format | ||||
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Contributor
There was a problem hiding this comment. You can determine the input format from
Author
There was a problem hiding this comment. Comment also relevant to #7443 (comment) The problem I have with this is that if it is a nexus or phylip file, their extension doesn't always tell whether it is an interleaved or sequential format. Even if you sniff it as an interleaved does $input_files.ext return phlyip-int or something like that which differentiates it from normal phylip? Otherwise I'm pretty sure amas needs the user to explicitly set the file format as an input. What are you thoughts on only taking non-interleaved formats, and give a warning to the user that it will not accept interleaved in the help or something? Following this also removing the option to output it as an interleaved file? Problem I see with this is that they can still upload an interleaved file since they have the same extension.
Contributor
There was a problem hiding this comment. I would suggest to leave it for now work on an extension of the datatypes. Do you think the inserleaved / sequential datatypes are well defined? Are you interested in working on this. I could try to give you some pointers.
Contributor
There was a problem hiding this comment. Alternatively we could also implement a small helper script that checks if the data is interleaved. Seems rather trivial.
Author
There was a problem hiding this comment. Yeh I could give the extension of the datatypes a shot. For phylipSince the header is a required field and gives the number of taxa, how about getting the name of the first taxa on the line following the header, then checking the line e.g. Then we would get the number of taxa at line 0 ( Actually could just get the length of the sequence length at line 1, and if it is less than the sequence length given ( For nexusLike you said it'll be more complicated; I'm not sure whether the header requires the number of taxa. I'll need to ask someone else to confirm or maybe you know someone else, but for a start given these examples: or If Let me know your thoughts.
Contributor
There was a problem hiding this comment. The examples for phylip at wikipedia https://en.wikipedia.org/wiki/PHYLIP also seem to allow interleaved format where the 2nd block does not list the species names again. So I guess the best criterion is the number of non-header lines. If there is more lines then taxa it should be interleaved. For nexus I would trust
Author
There was a problem hiding this comment. I've drafted a small helper function in this commit. There is also the next commit that makes it cleaner but less informative. Could you have a look and give any feedback any better ways to structure it? Regarding extension of the datatypes, could you give some pointers on how it would be best structured?
Author
There was a problem hiding this comment. I've changed the helper script so that the whole file isn't loaded in and instead is iterated through line by line and exited when the condition is met. One question, is there any need to check all files are all interleaved/sequential? Should this check be moved somewhere else, and for this script we just assume format based on the first file to make it faster?
Contributor
There was a problem hiding this comment.
I guess the we can check all files. |
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| --out-format $out_format | ||||
| --in-files | ||||
| @INPUT_FILENAMES@ | ||||
| --in-format $in_format | ||||
| --data-type $data_type | ||||
| --cores "\${GALAXY_SLOTS:-1}" | ||||
| $check_align | ||||
| ]]></command> | ||||
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| <inputs> | ||||
| <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequences to concatenate" multiple="true" | ||||
| help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." /> | ||||
| <expand macro="input_format" /> | ||||
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Analogous in all commands. |
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| <expand macro="output_format" label="Select output format for concatenated alignment" /> | ||||
| <param name="part_format" type="select" label="Format of the partitions file" | ||||
| help="A file defining how the concatenated alignment is split into separate gene/locus regions. Each line specifies a partition name and its position range (e.g., 'gene1 = 1-500' or 'DNA, gene1 = 1-500' for RAxML format)."> | ||||
| <option value="nexus">nexus</option> | ||||
| <option value="raxml">raxml</option> | ||||
| <option value="unspecified" selected="true">unspecified</option> | ||||
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| </param> | ||||
| <expand macro="data_type" /> | ||||
| <expand macro="check_align" /> | ||||
| </inputs> | ||||
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| <outputs> | ||||
| <data name="output" from_work_dir="concatenated.out" format="txt" label="${tool.name} on ${on_string} (Concatenated alignment)"> | ||||
| <change_format> | ||||
| <when input="out_format" value="fasta" format="fasta" /> | ||||
| <when input="out_format" value="phylip" format="phylip" /> | ||||
| <when input="out_format" value="phylip-int" format="phylip" /> | ||||
| <when input="out_format" value="nexus" format="nex" /> | ||||
| <when input="out_format" value="nexus-int" format="nex" /> | ||||
| </change_format> | ||||
| </data> | ||||
| <data name="partitions_out" from_work_dir="partitions.txt" format="txt" label="${tool.name} on ${on_string} (Partition file)" /> | ||||
| </outputs> | ||||
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| <tests> | ||||
| <test expect_num_outputs="2"> | ||||
| <param name="input_files" value="inputs/concat_1.fasta,inputs/concat_2.fasta" /> | ||||
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| <param name="out_format" value="phylip" /> | ||||
| <param name="part_format" value="nexus" /> | ||||
| <param name="in_format" value="fasta" /> | ||||
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| <param name="data_type" value="dna" /> | ||||
| <param name="check_align" value="false" /> | ||||
| <output name="output" file="outputs/expected_concat.phylip" ftype="phylip" compare="sim_size" /> | ||||
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| <output name="partitions_out" file="outputs/expected_partitions.txt" ftype="txt" /> | ||||
| </test> | ||||
| <test expect_num_outputs="2"> | ||||
| <param name="input_files" value="inputs/concat_1.fasta,inputs/concat_2.fasta" /> | ||||
| <param name="out_format" value="fasta" /> | ||||
| <param name="part_format" value="raxml" /> | ||||
| <param name="in_format" value="fasta" /> | ||||
| <param name="data_type" value="dna" /> | ||||
| <param name="check_align" value="false" /> | ||||
| <output name="output" file="outputs/expected_concat_fasta.fas" ftype="fasta" compare="sim_size" /> | ||||
| <output name="partitions_out" file="outputs/expected_partitions_raxml.txt" ftype="txt" /> | ||||
| </test> | ||||
| </tests> | ||||
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| <help><![CDATA[ | ||||
| **What it does** | ||||
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| AMAS Concat combines multiple sequence alignments into a single concatenated alignment, commonly used in phylogenomic analyses. | ||||
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| **Inputs** | ||||
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| - **Multiple alignment files**: Select 2 or more pre-aligned sequence files (FASTA, PHYLIP, or NEXUS format) | ||||
| - **Input format**: Specify the format of your input files | ||||
| - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences | ||||
| - **Output format**: Select the desired format for the concatenated alignment | ||||
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| **Outputs** | ||||
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| 1. **Concatenated alignment**: A single file containing all input alignments joined end-to-end | ||||
| 2. **Partitions file**: Defines the boundaries of each original alignment within the concatenated file | ||||
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| @PARTITIONS_HELP@ | ||||
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| **Use cases** | ||||
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| - **Multi-locus phylogenomics**: Combine hundreds of genes for species tree inference | ||||
| - **Partitioned phylogenetic analysis**: Apply different evolutionary models to different genes using tools like RAxML or IQ-TREE | ||||
| - **Supermatrix construction**: Create dataset for concatenation-based phylogenetic methods | ||||
| - **Increased phylogenetic signal**: Leverage information from multiple loci to resolve difficult nodes | ||||
| - **Comparative analyses**: Prepare datasets for testing hypotheses across multiple genomic regions | ||||
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| @AMAS_SHARED_HELP@ | ||||
| ]]></help> | ||||
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| <expand macro="citations" /> | ||||
| </tool> | ||||
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| <tool id="amas_remove" name="AMAS remove" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
| <description>remove taxa from multiple alignments</description> | ||
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| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
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| <xrefs> | ||
| <xref type="bio.tools">amas</xref> | ||
| </xrefs> | ||
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| <expand macro="requirements" /> | ||
| <expand macro="version_command" /> | ||
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| <command detect_errors="exit_code"><![CDATA[ | ||
| #import re | ||
| set -eu; | ||
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| @SYMLINK_INPUTS@ | ||
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| python -m amas.AMAS | ||
| remove | ||
| --taxa-to-remove | ||
| #for $taxon in $taxa_to_remove.split() | ||
| '$taxon' | ||
| #end for | ||
| --out-format $out_format | ||
| --in-files | ||
| @INPUT_FILENAMES@ | ||
| --in-format $in_format | ||
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| --data-type $data_type | ||
| --cores "\${GALAXY_SLOTS:-1}" | ||
| $check_align | ||
| ]]></command> | ||
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| <inputs> | ||
| <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequence(s) to remove taxa" multiple="true" | ||
| help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." /> | ||
| <expand macro="input_format" /> | ||
| <expand macro="output_format" label="Select output format for alignment(s) with taxa removed"/> | ||
| <param name="taxa_to_remove" type="text" label="Taxa to remove" | ||
| help="Space-separated list of taxon names to remove (e.g., 'OTU9 OTU10 Sample_A'). Note: AMAS converts spaces to underscores and strips quotes from sequence names, so use 'Species_1' to remove a taxon named 'Species 1'."> | ||
| <validator type="regex" message="Please provide at least one taxon name (alphanumeric, underscores, hyphens, and dots allowed)">[A-Za-z0-9_.\-]+(\s+[A-Za-z0-9_.\-]+)*</validator> | ||
| </param> | ||
| <expand macro="data_type" /> | ||
| <expand macro="check_align" /> | ||
| </inputs> | ||
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| <outputs> | ||
| <expand macro="collection_outputs" name="reduced_alignments" /> | ||
| </outputs> | ||
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| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_files" value="inputs/remove_input.nex" /> | ||
| <param name="taxa_to_remove" value="OTU9 OTU10" /> | ||
| <param name="out_format" value="nexus-int" /> | ||
| <param name="in_format" value="nexus" /> | ||
| <param name="data_type" value="dna" /> | ||
| <param name="check_align" value="false" /> | ||
| <output_collection name="reduced_alignments_nexus" type="list"> | ||
| <element name="reduced_remove_input.nex-out.int-nex" file="outputs/expected_remove_filtered.int-nex" ftype="nex" /> | ||
| </output_collection> | ||
| </test> | ||
| </tests> | ||
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| <help><![CDATA[ | ||
| **What it does** | ||
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| AMAS Remove excludes specified taxa (sequences) from one or more alignments. This is useful for removing problematic sequences, outgroups, or creating taxon subsets for comparative analyses. | ||
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| **Inputs** | ||
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| - **Alignment files**: One or more pre-aligned sequence files (FASTA, PHYLIP, or NEXUS format) | ||
| - **Taxa to remove**: Space-separated list of sequence names to exclude (e.g., 'OTU9 OTU10 Sample_A') | ||
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| **Important**: AMAS converts spaces to underscores and strips quotes from sequence names during processing. If your input file contains a taxon named 'Species 1' or '"Species 1"', you must specify it as 'Species_1' in the taxa to remove list. | ||
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| - **Input format**: Specify the format of your input files | ||
| - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences | ||
| - **Output format**: Select the desired format for the reduced alignments | ||
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| **Outputs** | ||
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| A collection of alignment files with specified taxa removed. Each output file contains the same alignment as the input, minus the excluded sequences. | ||
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| **Tip:** You may want to realign your files after taxon removal. | ||
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| **Use cases** | ||
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| - Remove sequences with excessive missing data | ||
| - Exclude contaminated or mis-identified samples | ||
| - Create taxon subsets for sensitivity analyses | ||
| - Remove outgroups after tree rooting | ||
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| @AMAS_SHARED_HELP@ | ||
| ]]></help> | ||
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| <expand macro="citations" /> | ||
| </tool> | ||
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| <tool id="amas_replicate" name="AMAS replicate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
| <description>replicate multiple alignments</description> | ||
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| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
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| <xrefs> | ||
| <xref type="bio.tools">amas</xref> | ||
| </xrefs> | ||
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| <expand macro="requirements" /> | ||
| <expand macro="version_command" /> | ||
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| <command detect_errors="exit_code"><![CDATA[ | ||
| #import re | ||
| set -eu; | ||
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| @SYMLINK_INPUTS@ | ||
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| python -m amas.AMAS | ||
| replicate | ||
| --rep-aln $replicate_replicates $replicate_loci | ||
| --out-format $out_format | ||
| --in-files | ||
| @INPUT_FILENAMES@ | ||
| --in-format $in_format | ||
| --data-type $data_type | ||
| --cores "\${GALAXY_SLOTS:-1}" | ||
| $check_align | ||
| ]]></command> | ||
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| <inputs> | ||
| <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequence(s) to replicate" multiple="true" | ||
| help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." /> | ||
| <expand macro="input_format" /> | ||
| <expand macro="output_format" label="Select output format for replicated alignment(s)" /> | ||
| <param name="replicate_replicates" type="integer" value="10" min="1" label="Number of replicate datasets to build" /> | ||
| <param name="replicate_loci" type="integer" value="2" min="1" label="Number of loci per replicate" /> | ||
| <expand macro="data_type" /> | ||
| <expand macro="check_align" /> | ||
| </inputs> | ||
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| <outputs> | ||
| <expand macro="collection_outputs" name="replicate_alignments" /> | ||
| </outputs> | ||
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| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_files" value="inputs/fasta1.fas" /> | ||
| <param name="replicate_replicates" value="2" /> | ||
| <param name="replicate_loci" value="1" /> | ||
| <param name="out_format" value="nexus" /> | ||
| <param name="in_format" value="fasta" /> | ||
| <param name="data_type" value="dna" /> | ||
| <param name="check_align" value="false" /> | ||
| <output_collection name="replicate_alignments_nexus" type="list"> | ||
| <element name="replicate1_1-loci-out.nex" file="outputs/expected_replicate1.nex" ftype="nex" /> | ||
| <element name="replicate2_1-loci-out.nex" file="outputs/expected_replicate2.nex" ftype="nex" /> | ||
| </output_collection> | ||
| </test> | ||
| </tests> | ||
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| <help><![CDATA[ | ||
| **What it does** | ||
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| AMAS Replicate generates jackknife or bootstrap replicates by randomly sampling loci (genes) from your dataset. This is used to assess phylogenetic signal distribution and node support across different genomic regions. | ||
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| **Inputs** | ||
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| - **Alignment files**: Multiple pre-aligned sequence files, one per locus/gene (FASTA, PHYLIP, or NEXUS format) | ||
| - **Number of replicates**: How many replicate datasets to generate | ||
| - **Loci per replicate**: How many loci to include in each replicate | ||
| - **Input format**: Specify the format of your input files | ||
| - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences | ||
| - **Output format**: Select the desired format for the replicate alignments | ||
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| **Outputs** | ||
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| A collection of replicate alignment files. Each replicate contains a random subset of the input loci concatenated together. | ||
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| **Use cases** | ||
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| - **Phylogenetic jackknifing**: Assess whether phylogenetic signal is driven by specific loci | ||
| - **Node support evaluation**: Test robustness of tree topology across different gene combinations | ||
| - **Signal heterogeneity**: Identify whether conflicting signals come from particular genomic regions | ||
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| **Example** | ||
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| From 100 input genes, create 10 replicates each containing 50 randomly sampled genes. Each replicate can then be used to build a phylogenetic tree, and consistency across replicates indicates robust phylogenetic signal. | ||
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| @AMAS_SHARED_HELP@ | ||
| ]]></help> | ||
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| <expand macro="citations" /> | ||
| </tool> |
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