--- a/instagraal.xml	Thu Nov 10 14:36:10 2022 +0000
+++ b/instagraal.xml	Sun Nov 13 12:59:17 2022 +0000
@@ -28,11 +28,11 @@
 ln -s '$fragments_list' hic_folder/fragments_list.txt &&
 ln -s '$info_contigs' hic_folder/info_contigs.txt &&
 
-#if $reference_genome.source == 'history':
+#if $ref_source.source == "history"
     #set $ref_genome = 'reference.fasta'
-    ln -s -f '${reference_genome.history_item}' $ref_genome &&
-#else:
-    #set $ref_genome = $reference_genome.index.fields.path
+    ln -s '${ref_source.ref_fasta}' $ref_genome &&
+#elif $ref_source.source == "builtin"
+   #set $ref_genome = '${ref_source.ref_fasta_builtin.fields.path}'
 #end if
 
 instagraal
@@ -70,22 +70,19 @@
         <param name="fragments_list" type="data" format="tabular" label="Fragments list"/>
         <param name="info_contigs" type="data" format="tabular" label="info_contigs"/>
 
-        <conditional name="reference_genome">
-            <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
-                <option value="indexed" selected="true">Use a built-in genome</option>
-                <option value="history">Use a genome from history</option>
+        <conditional name="ref_source">
+            <param type="select" name="source" label="Reference genome source">
+                <option value="history" selected="true">History</option>
+                <option value="builtin">Built-in</option>
             </param>
-            <when value="indexed">
-                <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
-                    <options from_data_table="fasta_indexes">
-                        <filter type="sort_by" column="2" />
-                        <validator type="no_options" message="No genomes are available for the selected input dataset" />
-                    </options>
+            <when value="history">
+                <param type="data" format="fasta" name="ref_fasta" label="Reference genome" />
+            </when>
+            <when value="builtin">
+                <param type="select" name="ref_fasta_builtin" label="Reference genome">
+                    <options from_data_table="all_fasta" />
                 </param>
             </when>
-            <when value="history">
-                <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
-            </when>
         </conditional>
 
         <param argument="--level" type="integer" value="4" min="3" max="6" label="Level (resolution) of the contact map"
@@ -116,9 +113,9 @@
             <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular" />
             <param name="fragments_list" value="fragments_list.tabular" />
             <param name="info_contigs" value="info_contigs.tabular" />
-            <conditional name="reference_genome">
+            <conditional name="ref_source">
                 <param name="source" value="history"/>
-                <param name="history_item" value="fake.fasta" />
+                <param name="ref_fasta" value="fake.fasta" />
             </conditional>
             <assert_command>
                 <has_text text="NNNNNNNNNN"/> <!--  10 long, the default -->

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Sun Nov 13 12:59:17 2022 +0000
@@ -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.
+#

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Sun Nov 13 12:59:17 2022 +0000
@@ -0,0 +1,13 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of indexes in the hisat mapper format -->
+    <table name="hisat2_indexes" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/hisat2_indexes.loc" />
+    </table>
+</tables>