--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Wed Mar 19 10:51:45 2014 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Fri Oct 31 11:43:23 2014 -0400
@@ -113,8 +113,9 @@
         <stdio>
             <!-- Anything other than zero is an error -->
             <exit_code range="1:" />
+            <!-- Might see negative return codes for Unix signals via Python subprocess -->
             <exit_code range=":-1" />
-            <!-- In case the return code has not been set propery check stderr too -->
+            <!-- In case the return code has not been set properly check stderr too -->
             <regex match="Error:" />
             <regex match="Exception:" />
         </stdio>
@@ -321,8 +322,42 @@
             <when value="advanced">
                 <yield />
             </when>
-        </conditional>        
+        </conditional>
     </xml>
+    <xml name="advanced_optional_id_files">
+        <conditional name="adv_optional_id_files_opts">
+            <param name="adv_optional_id_files_opts_selector" type="select"
+                   label="Restrict search of database to a given set of ID's"
+		   help="This feature provides a means to exclude ID's from a BLAST database search. The expectation values in the BLAST results are based upon the sequences actually searched, and not on the underlying database. Note this cannot be used when comparing against a FASTA file.">
+                <option value="none" selected="True">No restriction, search the entire database</option>
+                <option value="gilist">GI identifers</option>
+                <option value="negative_gilist">Negative GI identifers</option>
+                <option value="seqidlist">Sequence identifers (SeqId's)</option>
+            </param>
+            <when value="none" />
+            <when value="gilist">
+                <param name="gilist" type="data" format="txt" label="Restrict search of database to GI's listed in this file"
+                       help="This option is only available for database searches."/>
+            </when>
+            <when value="negative_gilist">
+                <param name="negative_gilist" type="data" format="txt" label="Restrict search of database to everything except the GI's listed in this file"
+                       help="This option is only available for database searches."/>
+            </when>
+            <when value="seqidlist">
+                <param name="seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId's"
+                       help="This option is only available for database searches."/>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@ADV_ID_LIST_FILTER@">
+#if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist':
+    -negative_gilist $adv_opts.adv_optional_id_files_opts.negative_gilist
+#elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'gilist':
+    -gilist $adv_opts.adv_optional_id_files_opts.gilist
+#elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'seqidlist':
+    -seqidlist $adv_opts.adv_optional_id_files_opts.seqidlist
+#end if
+    </token>
     <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token>
     <token name="@BLAST_DB_SUBJECT@">
 #if $db_opts.db_opts_selector == "db":
@@ -379,6 +414,13 @@
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
     </token>
+    <xml name="blast_citations">
+        <citations>
+            <citation type="doi">10.1186/1471-2105-10-421</citation>
+            <citation type="doi">10.7717/peerj.167</citation>
+            <!-- TODO: Add BibTeX entry / preprint DOI for Galaxy BLAST+ paper -->
+        </citations>
+    </xml>
     <token name="@OUTPUT_FORMAT@">**Output format**
 
 Because Galaxy focuses on processing tabular data, the default output of this