Metadata
All objects
All metadata objects support the following fields:
Field
Supported values
Description
created*
Date of creation
updated*
Date of last update
* Mandatory
Projects
The following metadata fields are recognized by different interfaces for Projects:
Project Features
Metadata with additional information and features about the project:
Field
Supported values
Description
comments
String
Free-form comments
description
String
Free-form description
name*
Name‡
* Mandatory
Project System Metadata
Metadata entries automatically set by MiGA:
Field
Supported values
Description
datasets*
Array of String
List of datasets in the project
type*
String
* Mandatory
‡ By default the base name of the project path
Project Flags
Metadata entries that trigger specific behaviors in MiGA:
Field
Supported values
Description
ref_project
Path
Project with reference taxonomy
db_proj_dir
Path
Directory containing database projects
tax_pvalue
Float [0,1]
Max p-value to transfer taxonomy (def: 0.05)
aai_p
String
Value of aai.rb -p° on AAI (def: blast+)
haai_p
String
Value of aai.rb -p° on hAAI (def: blast+)
ani_p
String
Value of ani.rb -p° on ANI (def: blast+)
max_try
Integer
Max number of task attempts (def: 10)
aai_save_rbm
Boolean
Should RBMs be saved for OGS analysis?
ogs_identity
Float [0,100]
Min RBM identity for OGS (def: 80)
clean_ogs
Boolean
If false, keeps ABC (clades only)
run_clades
Boolean
Should clades be estimated from distances?
gsp_ani
Float [0,100]
ANI limit to propose gsp clades (def: 90)
gsp_aai
Float [0,100]
AAI limit to propose gsp clades (def: 95)
gsp_metric
String
Metric to propose clades: ani
(def), aai
ess_coll
String
Collection of essential genes to use+
min_qual
Float (or 'no')
Min. genome quality (or no filter; def: 25)
° By default:
blast+
. Other supported values:blast
,blat
,diamond
(except for ANI), andfastani
(only for ANI),no
(only for hAAI). If usingdiamond
and/orfastani
, the corresponding software must be installed. Important: These defaults will change in v1.0 to:blast+
for hAAI,diamond
for AAI, andfastani
for ANI.+ One of:
dupont_2012
(default), orlee_2019
Project Hooks
Additionally, hooks can be defined for projects as arrays of arrays containing the action name and the arguments (if any). For example, one can define:
or
Supported events:
on_create()
: When createdon_load()
: When loadedon_save()
: When savedon_add_dataset(object)
: When a dataset is added, with nameobject
on_unlink_dataset(object)
: When dataset with nameobject
is unlinkedon_result_ready(object)
: When any result is ready, with keyobject
on_result_ready_{result}()
: Whenresult
is readyon_processing_ready()
: When processing is complete
Supported hooks:
run_lambda(lambda, args...)
run_cmd(cmd)
Datasets
The following metadata fields are recognized by different interfaces for Datasets:
Dataset Features
Metadata with additional information and features about the dataset:
Field
Supported values
Description
tax
MiGA::Taxonomy
Taxonomy of the dataset
quality
String
Description of genome quality
dprotologue
String
Taxonumber in the Digital Protologue DB
ncbi_tax_id
String
Linking ID(s)‡ for NCBI Taxonomy
ncbi_nuccore
String
Linking ID(s)‡ for NCBI Nucleotide
ncbi_asm
String
Linking ID(s)‡ for NCBI Assembly
ebi_embl
String
Linking ID(s)‡ for EBI EMBL
ebi_ena
String
Linking ID(s)‡ for EBI ENA
web_assembly
String
URL to download assembly
web_assembly_gz
String
URL to download gzipped assembly
see_also
String
Link(s)‡ in the format text:url
is_type
Boolean
If it is type material
is_ref_type
Boolean
If it is reference material°
type_rel
String
Relationship to type material
suspect
Array(String)
Flags indicating a suspect dataset
‡ Multiple values can be provided separated by commas or colons
Dataset System Metadata
Metadata entries automatically set by MiGA:
Field
Supported values
Description
type*
String
ref
Boolean
inactive
Boolean
If auto-processing should stop
metadata_only
Boolean
Dataset with metadata but without input data
status
String
Proc. status: complete, incomplete, inactive
_step
String
For internal control of processing
_try_step
Integer
For internal control of processing
user
String
Deprecated
* Mandatory
Dataset Flags
Metadata entries that trigger specific behaviors in MiGA:
Field
Supported values
Description
run_step
Boolean
Forces running or not step
db_project
Path
Project to use as database
dist_req
Array of String
Run distances against these datasets*
* When searching best-matching datasets, include these datasets even if they are not visited using the medoid tree
Dataset Hooks
Supported events:
on_load()
: When loadedon_save()
: When savedon_remove()
: When removedon_inactivate()
: When inactivatedon_activate()
: When activatedon_result_ready(object)
: When any result is ready, with keyobject
on_result_ready_{result}()
: Whenresult
is readyon_preprocessing_ready()
: When preprocessing is complete
Supported hooks:
run_lambda(lambda, args...)
clear_run_counts()
run_cmd(cmd)
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