diff --git a/doc/source/_api_quickstart.rst b/doc/source/_api_quickstart.rst
new file mode 100644
index 00000000000..309850b5089
--- /dev/null
+++ b/doc/source/_api_quickstart.rst
@@ -0,0 +1,186 @@
+Quickstart
+==========
+
+Log in as your user, navigate to the API Keys page in the User menu, and
+generate a new API key.  Make a note of the API key, and then pull up a
+terminal.  Now we'll use the display.py script in your galaxy/scripts/api
+directory for a short example::
+
+        % ./display.py my_key http://localhost:4096/api/histories
+        Collection Members
+        ------------------
+        #1: /api/histories/8c49be448cfe29bc
+          name: Unnamed history
+          id: 8c49be448cfe29bc
+        #2: /api/histories/33b43b4e7093c91f
+          name: output test
+          id: 33b43b4e7093c91f
+
+The result is a Collection of the histories of the user specified by the API
+key (you).  To look at the details of a particular history, say #1 above, do
+the following::
+
+        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc
+        Member Information
+        ------------------
+        state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
+        state: ok
+        contents_url: /api/histories/8c49be448cfe29bc/contents
+        id: 8c49be448cfe29bc
+        name: Unnamed history
+
+This gives detailed information about the specific member in question, in this
+case the History.  To view history contents, do the following::
+
+
+        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents
+        Collection Members
+        ------------------
+        #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
+          name: Pasted Entry
+          type: file
+          id: 6f91353f3eb0fa4a
+
+What we have here is another Collection of items containing all of the datasets
+in this particular history.  Finally, to view details of a particular dataset
+in this collection, execute the following::
+
+        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
+        Member Information
+        ------------------
+        misc_blurb: 1 line
+        name: Pasted Entry
+        data_type: txt
+        deleted: False
+        file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
+        state: ok
+        download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
+        visible: True
+        genome_build: ?
+        model_class: HistoryDatasetAssociation
+        file_size: 17
+        metadata_data_lines: 1
+        id: 6f91353f3eb0fa4a
+        misc_info: uploaded txt file
+        metadata_dbkey: ?
+
+And now you've successfully used the API to request and select a history,
+browse the contents of that history, and then look at detailed information
+about a particular dataset.
+
+For a more comprehensive Data Library example, set the following option in your
+galaxy.ini as well, and restart galaxy again::
+
+        admin_users = you@example.org
+        library_import_dir = /path/to/some/directory
+
+In the directory you specified for 'library_import_dir', create some
+subdirectories, and put (or symlink) files to import into Galaxy into those
+subdirectories.
+
+In Galaxy, create an account that matches the address you put in 'admin_users',
+then browse to that user's preferences and generate a new API Key.  Copy the
+key to your clipboard and then use these scripts::
+
+        % ./display.py my_key http://localhost:4096/api/libraries
+        Collection Members
+        ------------------
+
+        0 elements in collection
+
+        % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library'
+        Response
+        --------
+        /api/libraries/f3f73e481f432006
+          name: api_test
+          id: f3f73e481f432006
+
+        % ./display.py my_key http://localhost:4096/api/libraries
+        Collection Members
+        ------------------
+        /api/libraries/f3f73e481f432006
+          name: api_test
+          id: f3f73e481f432006
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006
+        Member Information
+        ------------------
+        synopsis: None
+        contents_url: /api/libraries/f3f73e481f432006/contents
+        description: API Test Library
+        name: api_test
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
+        Collection Members
+        ------------------
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
+          name: /
+          type: folder
+          id: 28202595c0d2591f61ddda595d2c3670
+
+        % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
+        Response
+        --------
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
+          name: api_test_folder1
+          id: 28202595c0d2591fa4f9089d2303fd89
+
+        % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
+        Response
+        --------
+        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+          name: 2.bed
+          id: e9ef7fdb2db87d7b
+        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
+          name: 3.bed
+          id: 3b7f6a31f80a5018
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 
+        Collection Members
+        ------------------
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
+          name: /
+          type: folder
+          id: 28202595c0d2591f61ddda595d2c3670
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
+          name: /api_test_folder1
+          type: folder
+          id: 28202595c0d2591fa4f9089d2303fd89
+        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+          name: /api_test_folder1/2.bed
+          type: file
+          id: e9ef7fdb2db87d7b
+        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
+          name: /api_test_folder1/3.bed
+          type: file
+          id: 3b7f6a31f80a5018
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+        Member Information
+        ------------------
+        misc_blurb: 68 regions
+        metadata_endCol: 3
+        data_type: bed
+        metadata_columns: 6
+        metadata_nameCol: 4
+        uploaded_by: nate@...
+        metadata_strandCol: 6
+        name: 2.bed
+        genome_build: hg19
+        metadata_comment_lines: None
+        metadata_startCol: 2
+        metadata_chromCol: 1
+        file_size: 4272
+        metadata_data_lines: 68
+        message:
+        metadata_dbkey: hg19
+        misc_info: uploaded bed file
+        date_uploaded: 2010-06-22T17:01:51.266119
+        metadata_column_types: str, int, int, str, int, str
+
+Other parameters are valid when uploading, they are the same parameters as are
+used in the web form, like 'link_data_only' and etc.
+
+The request and response format should be considered alpha and are subject to change.
+
+
diff --git a/doc/source/api/quickstart.rst b/doc/source/api/quickstart.rst
new file mode 100644
index 00000000000..8e9043de638
--- /dev/null
+++ b/doc/source/api/quickstart.rst
@@ -0,0 +1,185 @@
+Quickstart
+==========
+
+Log in as your user, navigate to the API Keys page in the User menu, and
+generate a new API key.  Make a note of the API key, and then pull up a
+terminal.  Now we'll use the display.py script in your galaxy/scripts/api
+directory for a short example::
+
+        % ./display.py my_key http://localhost:4096/api/histories
+        Collection Members
+        ------------------
+        #1: /api/histories/8c49be448cfe29bc
+          name: Unnamed history
+          id: 8c49be448cfe29bc
+        #2: /api/histories/33b43b4e7093c91f
+          name: output test
+          id: 33b43b4e7093c91f
+
+The result is a Collection of the histories of the user specified by the API
+key (you).  To look at the details of a particular history, say #1 above, do
+the following::
+
+        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc
+        Member Information
+        ------------------
+        state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
+        state: ok
+        contents_url: /api/histories/8c49be448cfe29bc/contents
+        id: 8c49be448cfe29bc
+        name: Unnamed history
+
+This gives detailed information about the specific member in question, in this
+case the History.  To view history contents, do the following::
+
+
+        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents
+        Collection Members
+        ------------------
+        #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
+          name: Pasted Entry
+          type: file
+          id: 6f91353f3eb0fa4a
+
+What we have here is another Collection of items containing all of the datasets
+in this particular history.  Finally, to view details of a particular dataset
+in this collection, execute the following::
+
+        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
+        Member Information
+        ------------------
+        misc_blurb: 1 line
+        name: Pasted Entry
+        data_type: txt
+        deleted: False
+        file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
+        state: ok
+        download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
+        visible: True
+        genome_build: ?
+        model_class: HistoryDatasetAssociation
+        file_size: 17
+        metadata_data_lines: 1
+        id: 6f91353f3eb0fa4a
+        misc_info: uploaded txt file
+        metadata_dbkey: ?
+
+And now you've successfully used the API to request and select a history,
+browse the contents of that history, and then look at detailed information
+about a particular dataset.
+
+For a more comprehensive Data Library example, set the following option in your
+galaxy.ini as well, and restart galaxy again::
+
+        admin_users = you@example.org
+        library_import_dir = /path/to/some/directory
+
+In the directory you specified for 'library_import_dir', create some
+subdirectories, and put (or symlink) files to import into Galaxy into those
+subdirectories.
+
+In Galaxy, create an account that matches the address you put in 'admin_users',
+then browse to that user's preferences and generate a new API Key.  Copy the
+key to your clipboard and then use these scripts::
+
+        % ./display.py my_key http://localhost:4096/api/libraries
+        Collection Members
+        ------------------
+
+        0 elements in collection
+
+        % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library'
+        Response
+        --------
+        /api/libraries/f3f73e481f432006
+          name: api_test
+          id: f3f73e481f432006
+
+        % ./display.py my_key http://localhost:4096/api/libraries
+        Collection Members
+        ------------------
+        /api/libraries/f3f73e481f432006
+          name: api_test
+          id: f3f73e481f432006
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006
+        Member Information
+        ------------------
+        synopsis: None
+        contents_url: /api/libraries/f3f73e481f432006/contents
+        description: API Test Library
+        name: api_test
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
+        Collection Members
+        ------------------
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
+          name: /
+          type: folder
+          id: 28202595c0d2591f61ddda595d2c3670
+
+        % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
+        Response
+        --------
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
+          name: api_test_folder1
+          id: 28202595c0d2591fa4f9089d2303fd89
+
+        % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
+        Response
+        --------
+        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+          name: 2.bed
+          id: e9ef7fdb2db87d7b
+        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
+          name: 3.bed
+          id: 3b7f6a31f80a5018
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 
+        Collection Members
+        ------------------
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
+          name: /
+          type: folder
+          id: 28202595c0d2591f61ddda595d2c3670
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
+          name: /api_test_folder1
+          type: folder
+          id: 28202595c0d2591fa4f9089d2303fd89
+        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+          name: /api_test_folder1/2.bed
+          type: file
+          id: e9ef7fdb2db87d7b
+        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
+          name: /api_test_folder1/3.bed
+          type: file
+          id: 3b7f6a31f80a5018
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+        Member Information
+        ------------------
+        misc_blurb: 68 regions
+        metadata_endCol: 3
+        data_type: bed
+        metadata_columns: 6
+        metadata_nameCol: 4
+        uploaded_by: nate@...
+        metadata_strandCol: 6
+        name: 2.bed
+        genome_build: hg19
+        metadata_comment_lines: None
+        metadata_startCol: 2
+        metadata_chromCol: 1
+        file_size: 4272
+        metadata_data_lines: 68
+        message:
+        metadata_dbkey: hg19
+        misc_info: uploaded bed file
+        date_uploaded: 2010-06-22T17:01:51.266119
+        metadata_column_types: str, int, int, str, int, str
+
+Other parameters are valid when uploading, they are the same parameters as are
+used in the web form, like 'link_data_only' and etc.
+
+The request and response format should be considered alpha and are subject to change.
+
diff --git a/doc/source/api_doc.rst b/doc/source/api_doc.rst
index 1a657105284..b8acafaac48 100644
--- a/doc/source/api_doc.rst
+++ b/doc/source/api_doc.rst
@@ -1,8 +1,6 @@
 Galaxy API Documentation
-************************
+========================
 
-Background
-==========
 In addition to being accessible through a web interface, Galaxy can also be
 accessed programmatically, through shell scripts and other programs. The web
 interface is appropriate for things like exploratory analysis, visualization,
@@ -20,191 +18,12 @@ The Galaxy API addresses these and other situations by exposing Galaxy
 internals through an additional interface, known as an Application Programming
 Interface, or API.
 
-Quickstart
-==========
 
-Log in as your user, navigate to the API Keys page in the User menu, and
-generate a new API key.  Make a note of the API key, and then pull up a
-terminal.  Now we'll use the display.py script in your galaxy/scripts/api
-directory for a short example::
+.. toctree::
+   :maxdepth: 3
 
-        % ./display.py my_key http://localhost:4096/api/histories
-        Collection Members
-        ------------------
-        #1: /api/histories/8c49be448cfe29bc
-          name: Unnamed history
-          id: 8c49be448cfe29bc
-        #2: /api/histories/33b43b4e7093c91f
-          name: output test
-          id: 33b43b4e7093c91f
+    Galaxy API Quickstart <api/quickstart>
 
-The result is a Collection of the histories of the user specified by the API
-key (you).  To look at the details of a particular history, say #1 above, do
-the following::
+    Galaxy API Guidelines <api/guidelines>
 
-        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc
-        Member Information
-        ------------------
-        state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
-        state: ok
-        contents_url: /api/histories/8c49be448cfe29bc/contents
-        id: 8c49be448cfe29bc
-        name: Unnamed history
-
-This gives detailed information about the specific member in question, in this
-case the History.  To view history contents, do the following::
-
-
-        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents
-        Collection Members
-        ------------------
-        #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
-          name: Pasted Entry
-          type: file
-          id: 6f91353f3eb0fa4a
-
-What we have here is another Collection of items containing all of the datasets
-in this particular history.  Finally, to view details of a particular dataset
-in this collection, execute the following::
-
-        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
-        Member Information
-        ------------------
-        misc_blurb: 1 line
-        name: Pasted Entry
-        data_type: txt
-        deleted: False
-        file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
-        state: ok
-        download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
-        visible: True
-        genome_build: ?
-        model_class: HistoryDatasetAssociation
-        file_size: 17
-        metadata_data_lines: 1
-        id: 6f91353f3eb0fa4a
-        misc_info: uploaded txt file
-        metadata_dbkey: ?
-
-And now you've successfully used the API to request and select a history,
-browse the contents of that history, and then look at detailed information
-about a particular dataset.
-
-For a more comprehensive Data Library example, set the following option in your
-galaxy.ini as well, and restart galaxy again::
-
-        admin_users = you@example.org
-        library_import_dir = /path/to/some/directory
-
-In the directory you specified for 'library_import_dir', create some
-subdirectories, and put (or symlink) files to import into Galaxy into those
-subdirectories.
-
-In Galaxy, create an account that matches the address you put in 'admin_users',
-then browse to that user's preferences and generate a new API Key.  Copy the
-key to your clipboard and then use these scripts::
-
-        % ./display.py my_key http://localhost:4096/api/libraries
-        Collection Members
-        ------------------
-
-        0 elements in collection
-
-        % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library'
-        Response
-        --------
-        /api/libraries/f3f73e481f432006
-          name: api_test
-          id: f3f73e481f432006
-
-        % ./display.py my_key http://localhost:4096/api/libraries
-        Collection Members
-        ------------------
-        /api/libraries/f3f73e481f432006
-          name: api_test
-          id: f3f73e481f432006
-
-        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006
-        Member Information
-        ------------------
-        synopsis: None
-        contents_url: /api/libraries/f3f73e481f432006/contents
-        description: API Test Library
-        name: api_test
-
-        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
-        Collection Members
-        ------------------
-        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
-          name: /
-          type: folder
-          id: 28202595c0d2591f61ddda595d2c3670
-
-        % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
-        Response
-        --------
-        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
-          name: api_test_folder1
-          id: 28202595c0d2591fa4f9089d2303fd89
-
-        % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
-        Response
-        --------
-        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
-          name: 2.bed
-          id: e9ef7fdb2db87d7b
-        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
-          name: 3.bed
-          id: 3b7f6a31f80a5018
-
-        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 
-        Collection Members
-        ------------------
-        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
-          name: /
-          type: folder
-          id: 28202595c0d2591f61ddda595d2c3670
-        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
-          name: /api_test_folder1
-          type: folder
-          id: 28202595c0d2591fa4f9089d2303fd89
-        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
-          name: /api_test_folder1/2.bed
-          type: file
-          id: e9ef7fdb2db87d7b
-        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
-          name: /api_test_folder1/3.bed
-          type: file
-          id: 3b7f6a31f80a5018
-
-        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
-        Member Information
-        ------------------
-        misc_blurb: 68 regions
-        metadata_endCol: 3
-        data_type: bed
-        metadata_columns: 6
-        metadata_nameCol: 4
-        uploaded_by: nate@...
-        metadata_strandCol: 6
-        name: 2.bed
-        genome_build: hg19
-        metadata_comment_lines: None
-        metadata_startCol: 2
-        metadata_chromCol: 1
-        file_size: 4272
-        metadata_data_lines: 68
-        message:
-        metadata_dbkey: hg19
-        misc_info: uploaded bed file
-        date_uploaded: 2010-06-22T17:01:51.266119
-        metadata_column_types: str, int, int, str, int, str
-
-Other parameters are valid when uploading, they are the same parameters as are
-used in the web form, like 'link_data_only' and etc.
-
-The request and response format should be considered alpha and are subject to change.
-
-.. include:: api/guidelines.rst
-
-.. include:: lib/galaxy.webapps.galaxy.api.rst
+    Galaxy API Documentation <lib/galaxy.webapps.galaxy.api>
diff --git a/doc/source/ts_api_doc.rst b/doc/source/ts_api_doc.rst
index f69a9483a26..99b6c8c1be6 100644
--- a/doc/source/ts_api_doc.rst
+++ b/doc/source/ts_api_doc.rst
@@ -1,8 +1,6 @@
 Tool Shed API Documentation
-***************************
+===========================
 
-Introduction
-============
 The Galaxy Tool Shed can be accessed programmatically using API described
 here via shell scripts and other programs.
 To interact with the API you first need to log in as your user, navigate
@@ -13,7 +11,7 @@ key you have to attach to every request as a parameter. Example:
 
     GET https://toolshed.g2.bx.psu.edu/api/repositories?q=fastq?key=SOME_KEY_HERE
 
+.. toctree::
+   :maxdepth: 3
 
-.. include:: api/guidelines.rst
-
-.. include:: lib/galaxy.webapps.tool_shed.api.rst
+    Toolshed API Documentation <lib/galaxy.webapps.tool_shed.api>