tripal_blast/tripal_blast.module

<?php
/**
 * @file
 * .module file of Tripal BLAST.
 */

use Drupal\Core\Url;

/**
 * Implements hook_theme().
 * Used by Tripal BLAST UI page.
 *
 * @see templates in /templates
 */
function tripal_blast_theme($existing, $type, $theme, $path) {  
  // Links rendered as a markup for the template file.
  $context_links = [
    // QUERY SEARCH TYPE:
    // blast/nucleotide, blast/protein.
    'link_nucleotide' => \Drupal::l(t('Nucleotide'), Url::fromRoute('tripal_blast.nucleotide')),
    'link_protein'  => \Drupal::l(t('Protein'), Url::fromRoute('tripal_blast.protein')),
    
    // NUCLEOTIDE PROGRAM:
    // blast/nucleotide/nucleotide, blast/nucleotide/protein.
    'link_blastn' => \Drupal::l(t('blastn'), Url::fromRoute('tripal_blast.nucleotide_nucleotide')),
    'link_blastx'   => \Drupal::l(t('blastx'), Url::fromRoute('tripal_blast.nucleotide_protein')),
    
    // PROTEIN PROGRAM:
    // blast/protein/nucleotide, blast/protein/protein.
    'link_tblastn'  => \Drupal::l(t('tblastn'), Url::fromRoute('tripal_blast.protein_nucleotide')),    
    'link_blastp' => \Drupal::l(t('blastp'), Url::fromRoute('tripal_blast.protein_protein')),
    
    // MISC/ADMIN. 
    'link_config' => '#',
    'link_jobs'    => '#',
    'link_nodeadd'  => '#',
    'link_dbadd'     => '#',
    'link_dbfields'   => '#',
  ];

  // Pass rendered links as variables and make available in the template file.
  $variables = [
    // Tripal BLAST UI page.
    'theme-tripal-blast-ui' => [
      'variables' => ['context_links' => $context_links],
      'template'  => 'template-tripal-blast-ui',
    ],
    // Tripal BLAST Configuration page.
    // Tripal BLAST Help page.
    'theme-tripal-blast-help' => [
      'variables' => ['context_links' => $context_links],
      'template'  => 'template-tripal-blast-help',
    ],
  ];

  return $variables;
}