tripal/base/tripal_views_setup/tripal_views_setup.module

<?php

require_once 'includes/tripal_views_setup.admin.inc';

function tripal_views_setup_menu(){
  $items = array();

  $items['admin/tripal/tripal_views_setup'] = array(
    'title' => t('Tripal Views Setups'),
    'description' => t('Tripal Views Setups settings page, allows you to select and create materialized views and chado tables to use for searches.'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_views_setup_admin_form'),
    // 'page callback' => 'tripal_views_setup_admin_form_page',
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
  );

  //page to actually create setup->mview->chado table relationships
   $items['admin/tripal/tripal_views_setup_new'] = array(
     'title' => 'Create New Views Setup',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_views_setup_new_setup_form'),
     'access arguments' => array('access administration pages'), //TODO: figure out the proper permissions arguments
     'type' => MENU_NORMAL_ITEM,
   );

   $items['admin/tripal/tripal_views_setup/ajax/mview_cols'] = array(
     'title' => 'Get MView Columns',
     'page callback' => 'tripal_view_setup_ajax_mview_cols',
     'access arguments' => array('access administration pages'),
     'type' => MENU_CALLBACK,
   );

  $items['admin/tripal/tripal_views_setup/ajax/field_col_join'] = array(
     'title' => 'Get Join Columns',
     'page callback' => 'tripal_view_setup_ajax_field_col_join',
     'access arguments' => array('access administration pages'),
     'type' => MENU_CALLBACK,
   );

  // $items['admin/tripal/tripal_views_setup_new/ajax/mview_column'] = array(
    // 'title' => 'Get Mview Columns',
    // 'page callback' => 'tripal_views_setup_ajax_db_mview_columns',
    // 'access arguments' => array('access administration pages'),
    // 'type' => MENU_CALLBACK,
  // );

  // $items['admin/tripal/tripal_views_setup_new/ajax/base_table_name'] = array(
    // 'title' => 'Get Chado Tables',
    // 'page callback' => 'tripal_views_setup_ajax_db_chado_tables',
    // 'access arguments' => array('access administration pages'),
    // 'type' => MENU_CALLBACK,
  // );

  return $items;
}

function tripal_views_setup_theme(){
  $theme = array();

//   $theme['tripal_views_setup_fields_form'] = array(
  $theme['tripal_views_setup_new_setup_form'] = array(
    'arguments' => array('form' => NULL),
      'template'  => 'tripal_views_setup_fields_form',
   );

  return $theme;
}