Registers a drush command and constructs the full help for that command

Return value

And array of command descriptions

Related topics

File

legacy/tripal_phylogeny/tripal_phylogeny.drush.inc, line 37

Contains function relating to drush-integration of this module.

Code

function tripal_phylogeny_drush_command() {
  $items = array();
  $items['trp-insert-phylotree'] = array(
    'description' => dt('Adds a new phylotree record.'),
    'arguments' => array(),
    'examples' => array(),
    'options' => array(
      'username' => array(
        'description' => dt('The Drupal user name for which the job should be run.  The permissions for this user will be used.'),
        'required' => TRUE,
      ),
      'name' => array(
        'description' => dt('The name of the tree. The name of the tree must be unique.'),
        'required' => TRUE,
      ),
      'description' => array(
        'description' => dt('A description for the tree. Use quotes.'),
        'required' => TRUE,
      ),
      'analysis' => array(
        'description' => dt('The name of the analysis used to generate this tree. This should be the name of an analysis record already present in Chado. Use quotes.'),
        'required' => TRUE,
      ),
      'leaf_type' => array(
        'description' => dt('The Sequence Ontology term for the leaf node type of the tree (e.g. polypeptide). If this is a taxonomic the use the word "taxonomy".'),
        'required' => TRUE,
      ),
      'tree_file' => array(
        'description' => dt('The full path to the file containing the tree.'),
        'required' => TRUE,
      ),
      'format' => array(
        'description' => dt('The format of the input file. Currently, only the "newick" file format is supported.'),
        'required' => TRUE,
      ),
      'dbxref' => dt('A database cross-reference of the form DB:ACCESSION. Where DB is the database name, which is already present in Chado, and ACCESSION is the unique identifier for this tree in the remote database.'),
      'sync' => dt('Set to 1 if this tree should be synced with Drupal.'),
      'match' => dt('Set to "uniquename" if the leaf nodes should be matched with the feature uniquename'),
      'name_re' => dt('If the leaf type is NOT "taxonomy", then this option can be a regular expression used pull out the name of the feature from the node label in theintput tree.'),
    ),
  );

  $items['trp-update-phylotree'] = array(
    'description' => dt('Adds a new phylotree record. If a new file is provided then the entire existing tree will be rebuilt using the file provided.'),
    'arguments' => array(),
    'examples' => array(),
    'options' => array(
      'username' => array(
        'description' => dt('The Drupal user name for which the job should be run.  The permissions for this user will be used.'),
        'required' => TRUE,
      ),
      'phylotree_id' => dt('The unique phylotree ID assigned within Chado for the tree that should be updated.'),
      'name' => dt('A unique name for the tree. If the phylotree_id is not provided then the phylotree matching this name will be updated.'),
      'description' => dt('A description for the tree. Use quotes.'),
      'analysis' => dt('The name of the analysis used to generate this tree. This should be the name of an analysis record already present in Chado. Use quotes.'),
      'leaf_type' => dt('The Sequence Ontology term for the leaf node type of the tree (e.g. polypeptide). If this is a taxonomic the use the word "taxonomy".'),
      'tree_file' => dt('The full path to the file containing the tree.'),
      'format' => dt('The format of the input file. Currently, only the "newick" file format is supported.'),
      'dbxref' => dt('A database cross-reference of the form DB:ACCESSION. Where DB is the database name, which is already present in Chado, and ACCESSION is the unique identifier for this tree in the remote database.'),
      'sync' => dt('Set to 1 if this tree should be synced with Drupal.'),
      'match' => dt('Set to "uniquename" if the leaf nodes should be matched with the feature uniquename'),
      'name_re' => dt('If the leaf type is NOT "taxonomy", then this option can be a regular expression used pull out the name of the feature from the node label in theintput tree.'),
    ),
  );

  $items['trp-delete-phylotree'] = array(
    'username' => array(
      'description' => dt('The Drupal user name for which the job should be run.  The permissions for this user will be used.'),
      'required' => TRUE,
    ),
    'description' => dt('Deletes a phylotree record and it\'s corresponding tree nodes.'),
    'arguments' => array(),
    'examples' => array(),
    'options' => array(
      'phylotree_id' => dt('The unique phylotree ID assigned within Chado for the tree that should be deleted.'),
      'name' => dt('If the phylotree_id is not provided then the phylotree matching this name will be deleted.'),
    ),
  );
  return $items;
}