From abad770d5a7ff7a49bd6c2aae61f54d5ed05e644 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 18 Apr 2024 18:55:38 +0200 Subject: [PATCH] change text in a minor way --- doc/source/admin/data_tables.md | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/doc/source/admin/data_tables.md b/doc/source/admin/data_tables.md index 2004261fc813..44f1cc008e72 100644 --- a/doc/source/admin/data_tables.md +++ b/doc/source/admin/data_tables.md @@ -1,12 +1,12 @@ # Tool data Galaxy stores tool data in the path defined by `tool_data_path` (by default `tool-data/`). -It's possible to separate tool data of ToolShed-installed tools by setting `shed_tool_data_path`. +It's possible to separate tool data of toolshed-installed tools by setting `shed_tool_data_path`. Tool data consists of: 1. the actual data -2. one or more so called `loc` files +2. one or more `loc` files 3. entries in a tool data table (config) file @@ -14,7 +14,7 @@ Tool data consists of: In order to understand the naming and structure of these three components it might be of advantage to look in the history. Tool data was organized in tabular `loc` that contained metadata and paths -of the data. Those files were were installed with the tool and could be accessed with the +of the data. Those files were installed with the tool and could be accessed with the [`from_file`](https://docs.galaxyproject.org/en/master/dev/schema.html#from-file) mechanism from tools. Since each tool version had it's own `loc` file the maintenance was difficult. With tool data tables an additional abstraction layer was introduced that is used from tools via @@ -29,7 +29,7 @@ setting `galaxy_data_manager_data_path`. ## `loc` files -In order to make tool data usable from Galaxy tools so called `loc` files are used. +In order to make tool data usable from Galaxy tools `loc` files are used. Those are tabular (by default tab separated) files with the extension `.loc`. Besides the actual paths, the entries can contain IDs, names, or other metadata that can be used in tools to select reference data. The paths should be given as absolute paths, @@ -40,8 +40,7 @@ are stored). By setting `shed_tool_data_path` this can be separated. ## Tool data tables The tool data tables that should be used in a Galaxy instance are listed -in tool data table config files. In addition these contain some -metadata. +in tool data table config files. In addition these contain metadata. Tool data table config files are XML files listing tool data table configurations: