Add fifth test for data table function

test-data/all_fasta.loc

@@ -0,0 +1,3 @@
+#<value>        <dbkey> <display_name>  <file_path>
+#
+three_human_mRNA	thmRNA	Three-Human-mRANs	${__HERE__}/three_human_mRNA.fasta

test-data/tool_data_table_conf.xml.test

@@ -12,4 +12,8 @@
         <columns>value, name, path</columns>
         <file path="${__HERE__}/blastdb_d.loc" />
     </table>
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/all_fasta.loc" />
+    </table>
 </tables>

tool-data/all_fasta.loc.sample

@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#

tool-data/tool_data_table_conf.xml.sample

@@ -11,4 +11,8 @@
         <columns>value, name, path</columns>
         <file path="tool-data/blastdb_d.loc" />
     </table>
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc.sample" />
+    </table>
 </tables>

tools/ncbi_blast_plus/ncbi_makeblastdb.xml

@@ -51,7 +51,7 @@ $hash_index
 ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful
 -title 'BLAST Database'
 #end if
--dbtype
+-dbtypne
 #if $input.type == "protein":
     prot
 #else:
@@ -231,8 +231,7 @@ $hash_index
                 <repeat name="selection">
                     <conditional name="nuc_choice">
                         <param name="source" value="history"/>
-                        <!--param name="source" value="cached"-->
-                            <param name="input_file" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />
+                        <param name="input_file" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />
                     </conditional> 
                 </repeat>
             </conditional> 
@@ -252,13 +251,13 @@ $hash_index
                 <extra_files type="file" value="three_human_mRNA.fasta.nsi" name="blastdb.nsi" />
             </output>
         </test>
-        <!--test>
+        <test>
             <conditional name="input">
                 <param name="type" value="nucleotide"/>
                 <repeat name="selection">
                     <conditional name="nuc_choice">
-                        <param name="source" value="cached">
-                            <param name="input_file" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />
+                        <param name="source" value="cached"/>
+                        <param name="input_file" value="three_human_mRNA" />
                     </conditional> 
                 </repeat>
             </conditional> 
@@ -277,7 +276,7 @@ $hash_index
                 <extra_files type="file" value="three_human_mRNA.fasta.nsd" name="blastdb.nsd" />
                 <extra_files type="file" value="three_human_mRNA.fasta.nsi" name="blastdb.nsi" />
             </output>
-        </test-->
+        </test>
     </tests>
     <help>
 **What it does**