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A PHP API for interacting with Galaxy
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GalaxyTools Class Reference

Public Member Functions

 __construct (GalaxyInstance $galaxy)
 
 index ($params)
 
 show ($params)
 
 diagnostics ($params)
 
 reload ($params)
 
 build ($params)
 
 citations ($params)
 
 download ($params)
 
 create ($params)
 

Constructor & Destructor Documentation

GalaxyTools::__construct ( GalaxyInstance  $galaxy)

The Tools constructor.

Parameters
GalaxyInstance$galaxyA GalaxyInstance object.
Returns
An instance of a Tools object.

Member Function Documentation

GalaxyTools::build (   $params)

Returns a tool model that includes its parameters. Returns a tool model including dynamic parameters and updated values.

Corresponds to the Galaxy API/path GET /api/tools/{tool_id}/build

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • tool_id: The id of the tool to perform this aciton on. Please use this class's index() function to retreive a tool id.
  • history_id: The id of the history to place the built tool. This parameter is required only if the authentication of the galaxy instance has been authenticated.
  • tool_version: Optional, the version of the tool.
Returns
An array containing the build model of the tool.
GalaxyTools::citations (   $params)

Retreive the citations for a given tool.

Corresponds to the Galaxy Api/path GET /api/tools/{tool_id}/citations

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • tool_id: The id of the specified tool. To obtain a tool id, please use this class' index() function.
Returns
An array containing infromation about the citations of the specified tool.
GalaxyTools::create (   $params)

Executes a tool using specified inputs.

Corresponds to the Galaxy API/path at POST /api/tools

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • tool_id: The id of the specified tool. To obtain a tool id, please use this class's index() function.
  • history_id: The history_id where the tool is located. To obtain history id's please see the history class.
  • files: Optional. an array of file infromation, the array should be NULL or in the following format:
    $params['files'] = array(
    0 => array(
    'name' => [file name],
    'path' => [full path to the file],
    ),
    1 => array(
    'name' => [file name],
    'path' => [full path to the file],
    ),
    ...
    );

input_dataset_ids: Optional. An array of dataset id's where the tool should grab its inputs from. Please see the datasets class to obtain id's. Each element of the array is itself an associative array with a key of 'id' containing the dataset ID and an optional 'src' key if the src is anything other than 'hda'.

  • tool_version: Optional, specify specific tool version for the tool.
  • region: Optional information on the region of the genome being rerun.
  • action: Optional, 'rerun' to rerun the tool and not execute
Returns
An array containing information about the created or executed tool.
GalaxyTools::diagnostics (   $params)

Return diagnostic information about a tool.

Corresponds to the Galaxy API/path at GET /api/tools/{tool_id}/diagnostics

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • tool_id: The id of the tool whos informaiton to obtain. To retreive a tool id please use this class's index funciton.
Returns
An array contaiing information about the diagnostics of a tool.
GalaxyTools::download (   $params)

Download a specified tool.

Corresponds to the Galaxy Api/Path at: GET /api/tools/{tool_id}/download

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • tool_id: The id of the specified tool. To obtain a tool id, please use this class's index() function.
  • file_path: The path to where the file will be stored.
Returns
Gzip of the tool.
GalaxyTools::index (   $params)

Retreive a list of tools defined by the parameters.

Corresponds to the Galaxy API/path: GET /api/tools:

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • tool_id: Optional, the id of the tool to specify.
  • q: Optional, additional search details.
  • in_panel: If TRUE, return tools marked as in panel.
  • trackster: If TRUE, return tools marked as trackster.
Returns
An array containing all the tools in galaxy that match the the specified search.
GalaxyTools::reload (   $params)

Reload specified tool.

Corresponds to the Galaxy Api/path GET /api/tools/{tool_id}/reload

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • tool_id: The id of the tool to reload.
Returns
An array of the tool that was reloaded.
GalaxyTools::show (   $params)

Retreives detailed informaiton of a specific tool.

Corresponds to the Galaxy API/path GET /api/tools/{tool_id}

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • tool_id: The id of the tool whos informaiton to obtain. To retreive a tool id please use this class's index funciton.
Returns
An array containing detailed information about a specific tool.
The documentation for this class was generated from the following file: