--- a/data_manager/malt_index_builder.xml	Tue Oct 12 14:15:35 2021 +0000
+++ b/data_manager/malt_index_builder.xml	Wed Oct 13 20:12:48 2021 +0000
@@ -10,40 +10,32 @@
 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
 --fasta_description '${all_fasta_source.fields.name}'
 --sequence_type '${sequence_type}'
+#if str($protein_reduct_setting_cond.protein_reduct_setting) == 'yes':
+    --protein_reduct '${protein_reduct_setting_cond.protein_reduct}'
+#end if
 #if str($seed_setting_cond.seed_setting) == 'yes':
     --shapes '${seed_setting_cond.shapes}'
-    --max_hits_per_seed $seed_setting_cond.max_hits_per_seed
-    --protein_reduct '${seed_setting_cond.protein_reduct}'
+    ## malt-build requires a string here.
+    --max_hits_per_seed '${seed_setting_cond.max_hits_per_seed}'
 #end if
     ]]></command>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta"/>
         </param>
-        <param name="sequence_name" type="text" value="" label="Name of sequence" />
-        <param name="sequence_id" type="text" value="" label="ID for sequence" />
-        <param  name="sequence_type" type="select" label="Specify whether the reference sequences are DNA or Protein sequences" help="Use the DNA setting For RNA sequences">
+        <param name="sequence_name" type="text" value="" label="Name of sequence"/>
+        <param name="sequence_id" type="text" value="" label="ID for sequence"/>
+        <param  name="sequence_type" type="select" label="Reference sequences type" help="Use the DNA setting For RNA sequences">
             <option value="DNA" selected="true">DNA</option>
             <option value="Protein">Protein</option>
         </param>
-        <conditional name="seed_setting_cond">
-            <param name="seed_setting" type="select" label="Specify seed settings?">
+        <conditional name="protein_reduct_setting_cond">
+            <param name="protein_reduct_setting" type="select" label="Specify protein alphabet resuction?" help="Used only if the reference sequences are Protein sequences">
                 <option selected="true" value="no">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="no"/>
             <when value="yes">
-                <param name="shapes" type="text" value="" label="Comma-separated list of seed shapes" help="See help text below">
-                    <sanitizer invalid_char="">
-                        <valid initial="string.printable">
-                            <remove value="&apos;" />
-                        </valid>
-                        <mapping initial="none">
-                            <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
-                        </mapping>
-                    </sanitizer>
-                </param>
-                <param name="max_hits_per_seed" type="integer" value="1" min="1" label="Maximum number of hits per seed"/>
                 <param name="protein_reduct" type="select" label="Name or definition of protein alphabet reduction">
                     <option selected="true" value="DIAMOND_11">DIAMOND_11</option>
                     <option value="BLOSUM50_10">BLOSUM50_10</option>
@@ -59,20 +51,59 @@
                 </param>
             </when>
         </conditional>
+        <conditional name="seed_setting_cond">
+            <param name="seed_setting" type="select" label="Specify seed settings?">
+                <option selected="true" value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="shapes" type="text" value="" label="Comma-separated list of seed shapes" help="See help text below">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.printable">
+                            <remove value="&apos;"/>
+                        </valid>
+                        <mapping initial="none">
+                            <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
+                        </mapping>
+                    </sanitizer>
+                </param>
+                <param name="max_hits_per_seed" type="integer" value="1" min="1" label="Maximum number of hits per seed"/>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
-        <data name="out_file" format="data_manager_json" />
+        <data name="out_file" format="data_manager_json"/>
     </outputs>
     <tests>
         <test>
             <param name="all_fasta_source" value="phiX174"/>
-            <output name="out_file" value="malt_index_builder.json"/>
+            <param name="sequence_name" value="Pretty name for phiX174"/>
+            <param name="sequence_id" value="phiX174-1"/>
+            <output name="out_file" value="malt_index_builder1.json"/>
+        </test>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <param name="sequence_name" value="Pretty name for phiX174"/>
+            <param name="sequence_id" value="phiX174-1"/>
+            <param name="seed_setting" value="yes"/>
+            <param name="shapes" value="111110111011110110111111"/>
+            <output name="out_file" value="malt_index_builder1.json"/>
+        </test>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <param name="sequence_name" value="Pretty name for phiX174"/>
+            <param name="sequence_id" value="phiX174-2"/>
+            <param name="sequence_type" value="Protein"/>
+            <param name="protein_reduct_setting" value="yes"/>
+            <param name="protein_reduct" value="BLOSUM50_10"/>
+            <output name="out_file" value="malt_index_builder2.json"/>
         </test>
     </tests>
     <help>
 .. class:: infomark
 
-**Notice:** Values for name, description, and id will be generated automatically if left blank.
+**Notice:** Values for Name and ID of sequence will be generated automatically if left blank.
 
 **What it does**