Mgnify Expanded Tools#

Configuration File: mgnify_expanded_tools.json Tool Type: Local Tools Count: 9

This page contains all tools defined in the mgnify_expanded_tools.json configuration file.

Available Tools#

MGnify_get_genome (Type: MGnifyExpandedTool)#

Get detailed genome information from the MGnify genome catalog. Returns assembly quality metrics …

MGnify_get_genome tool specification

Tool Information:

  • Name: MGnify_get_genome

  • Type: MGnifyExpandedTool

  • Description: Get detailed genome information from the MGnify genome catalog. Returns assembly quality metrics (completeness, contamination, N50), taxonomy, geographic origin, rRNA counts, protein count, pangenome statistics, and cross-references to ENA. Example: MGYG000000001 returns a high-quality Firmicutes isolate genome with 98.6% completeness.

Parameters:

  • genome_id (string) (required) MGnify genome accession. Examples: ‘MGYG000000001’, ‘MGYG000535630’.

Example Usage:

query = {
    "name": "MGnify_get_genome",
    "arguments": {
        "genome_id": "example_value"
    }
}
result = tu.run(query)

MGnify_get_go_terms (Type: MGnifyExpandedTool)#

Get a page of Gene Ontology annotations from a MGnify analysis, including accession, description,…

MGnify_get_go_terms tool specification

Tool Information:

  • Name: MGnify_get_go_terms

  • Type: MGnifyExpandedTool

  • Description: Get a page of Gene Ontology annotations from a MGnify analysis, including accession, description, count, and category. Response metadata exposes total_results, total_pages, has_more, and next_page; follow next_page to retrieve the complete annotation set.

Parameters:

  • analysis_id (string) (required) MGnify analysis accession (e.g., ‘MGYA00585482’). Find IDs via MGnify_list_analyses.

  • page (integer) (optional) One-based result page. Continue with metadata.next_page.

  • page_size (integer) (optional) Number of GO terms to return per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_get_go_terms",
    "arguments": {
        "analysis_id": "example_value"
    }
}
result = tu.run(query)

MGnify_get_interpro (Type: MGnifyExpandedTool)#

Get a page of InterPro protein-domain annotations from a MGnify analysis, including accession, de…

MGnify_get_interpro tool specification

Tool Information:

  • Name: MGnify_get_interpro

  • Type: MGnifyExpandedTool

  • Description: Get a page of InterPro protein-domain annotations from a MGnify analysis, including accession, description, and count. Response metadata exposes total_results, total_pages, has_more, and next_page; follow next_page to retrieve the complete annotation set.

Parameters:

  • analysis_id (string) (required) MGnify analysis accession (e.g., ‘MGYA00585482’). Find IDs via MGnify_list_analyses.

  • page (integer) (optional) One-based result page. Continue with metadata.next_page.

  • page_size (integer) (optional) Number of InterPro entries to return per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_get_interpro",
    "arguments": {
        "analysis_id": "example_value"
    }
}
result = tu.run(query)

MGnify_get_samples (Type: MGnifyExpandedTool)#

List MGnify biological samples with geographic, host, and environment provenance. Pass sample_acc…

MGnify_get_samples tool specification

Tool Information:

  • Name: MGnify_get_samples

  • Type: MGnifyExpandedTool

  • Description: List MGnify biological samples with geographic, host, and environment provenance. Pass sample_accession for one record, or omit it to page through samples filtered by study_accession or biome. List responses expose total_results, total_pages, has_more, and next_page; follow next_page to avoid first-page truncation.

Parameters:

  • sample_accession ([‘string’, ‘null’]) (optional) Fetch a single sample by its MGnify/ENA accession (e.g., ‘SRS10016989’). If provided, study_accession/biome/page are ignored.

  • study_accession ([‘string’, ‘null’]) (optional) Filter samples belonging to a study (e.g., ‘MGYS00002008’).

  • biome ([‘string’, ‘null’]) (optional) Filter by biome name lineage (e.g., ‘root:Host-associated:Human:Digestive system’).

  • page (integer) (optional) One-based result page for list mode. Continue with metadata.next_page.

  • page_size (integer) (optional) Samples per page in list mode (default 25, range 1-100).

Example Usage:

query = {
    "name": "MGnify_get_samples",
    "arguments": {
    }
}
result = tu.run(query)

MGnify_get_study_detail (Type: MGnifyExpandedTool)#

Get detailed information about a specific MGnify metagenomics study. Returns study name, abstract…

MGnify_get_study_detail tool specification

Tool Information:

  • Name: MGnify_get_study_detail

  • Type: MGnifyExpandedTool

  • Description: Get detailed information about a specific MGnify metagenomics study. Returns study name, abstract, associated BioProject, centre, public/private status, sample count, and biomes. Complementary to MGnify_search_studies which lists studies; use MGnify_list_analyses / MGnify_list_analysis_downloads for exact analyses/downloads counts (this endpoint does not provide them). Example: MGYS00002008 is a Tara Oceans marine metagenomics study.

Parameters:

  • study_accession (string) (required) MGnify study accession. Examples: ‘MGYS00002008’, ‘MGYS00005292’.

Example Usage:

query = {
    "name": "MGnify_get_study_detail",
    "arguments": {
        "study_accession": "example_value"
    }
}
result = tu.run(query)

MGnify_get_taxonomy (Type: MGnifyExpandedTool)#

Get a page of taxonomic composition from a MGnify analysis, including abundance, lineage, and ran…

MGnify_get_taxonomy tool specification

Tool Information:

  • Name: MGnify_get_taxonomy

  • Type: MGnifyExpandedTool

  • Description: Get a page of taxonomic composition from a MGnify analysis, including abundance, lineage, and rank. Supports SSU and LSU marker genes with strict validation. The response metadata exposes total_results, total_pages, has_more, and next_page; follow next_page to retrieve all taxa rather than silently stopping at the first page.

Parameters:

  • analysis_id (string) (required) MGnify analysis accession (e.g., ‘MGYA00585482’). Find IDs via MGnify_list_analyses.

  • rna_type (string) (optional) rRNA marker type: ‘ssu’ for 16S/18S (default) or ‘lsu’ for 23S/28S.

  • page (integer) (optional) One-based result page. Continue with metadata.next_page.

  • page_size (integer) (optional) Number of taxa to return per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_get_taxonomy",
    "arguments": {
        "analysis_id": "example_value"
    }
}
result = tu.run(query)

MGnify_list_analysis_downloads (Type: MGnifyExpandedTool)#

List a page of downloadable result files produced by a MGnify analysis, including file id, label/…

MGnify_list_analysis_downloads tool specification

Tool Information:

  • Name: MGnify_list_analysis_downloads

  • Type: MGnifyExpandedTool

  • Description: List a page of downloadable result files produced by a MGnify analysis, including file id, label/description, format, compression, group type, and direct URL. Response metadata exposes the exact file count, total_pages, has_more, and next_page; follow next_page to retrieve all files.

Parameters:

  • analysis_id (string) (required) MGnify analysis accession (e.g., ‘MGYA00585482’). Find IDs via MGnify_list_analyses.

  • page (integer) (optional) One-based result page. Continue with metadata.next_page.

  • page_size (integer) (optional) Number of download entries per page (default 100, range 1-100).

Example Usage:

query = {
    "name": "MGnify_list_analysis_downloads",
    "arguments": {
        "analysis_id": "example_value"
    }
}
result = tu.run(query)

MGnify_list_biomes (Type: MGnifyExpandedTool)#

Browse the MGnify biome hierarchy with explicit page pagination. Returns biome identifiers, names…

MGnify_list_biomes tool specification

Tool Information:

  • Name: MGnify_list_biomes

  • Type: MGnifyExpandedTool

  • Description: Browse the MGnify biome hierarchy with explicit page pagination. Returns biome identifiers, names, and sample counts. Response metadata exposes total_results, total_pages, has_more, and next_page so the complete hierarchy can be traversed.

Parameters:

  • depth (integer) (optional) Depth of the biome lineage to keep, counting ‘root’ as 1 (so ‘root:Engineered’ is 2 and ‘root:Host-associated:Human’ is 3). Filtered client-side because the MGnify API has no depth filter.

  • lineage (string) (optional) List this biome and all biomes below it, e.g. ‘root:Host-associated:Human’ (uses /biomes/{lineage}/children, which returns the biome itself plus every descendant, not only direct children). Combine with depth to keep one level. Omit to list all biomes.

  • page (integer) (optional) One-based result page. Continue with metadata.next_page.

  • page_size (integer) (optional) Results per page (default 25, range 1-100).

Example Usage:

query = {
    "name": "MGnify_list_biomes",
    "arguments": {
    }
}
result = tu.run(query)

MGnify_search_genomes (Type: MGnifyExpandedTool)#

Search the MGnify genome catalog by GTDB taxonomy lineage with explicit page pagination. Returns …

MGnify_search_genomes tool specification

Tool Information:

  • Name: MGnify_search_genomes

  • Type: MGnifyExpandedTool

  • Description: Search the MGnify genome catalog by GTDB taxonomy lineage with explicit page pagination. Returns genome quality metrics, taxonomy, and protein counts. Response metadata exposes total_results, total_pages, has_more, and next_page. Taxonomy names follow GTDB: use ‘Bacteroidota’, ‘Bacillota’, or ‘Pseudomonadota’ rather than older NCBI-style phylum names.

Parameters:

  • taxonomy (string) (optional) GTDB taxonomy lineage filter, matched anywhere in the lineage. Examples: ‘Bacteroidota’ (phylum), ‘Bacteroides’ (genus), ‘Bacillota’, ‘Pseudomonadota’. NCBI-style phylum names such as ‘Bacteroidetes’ or ‘Firmicutes’ return few or no hits – use the GTDB spelling.

  • page (integer) (optional) One-based result page. Continue with metadata.next_page.

  • page_size (integer) (optional) Results per page (default 25, range 1-100).

Example Usage:

query = {
    "name": "MGnify_search_genomes",
    "arguments": {
    }
}
result = tu.run(query)