--- a/chira_extract.xml	Thu May 07 03:37:33 2020 -0400
+++ b/chira_extract.xml	Fri May 29 06:57:01 2020 -0400
@@ -31,6 +31,10 @@
             -f2 '$reference.ref_fasta2'
         #end if
         $hybridize
+        $seed_interaction
+        $summarize
+        -a '$accessibility'
+        -m '$intarna_mode'
         -p "\${GALAXY_SLOTS:-2}"
         -o ./
     ]]></command>
@@ -86,24 +90,42 @@
                        help="Reference fasta file"/>
             </when>
         </conditional>
-        <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" />
+        <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
+               label="Hybridize chimeric loci?"
+               help="Turning this option on increases the run time of the tool significantly."/>
+        <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="false"
+               label="Enforce seed interaction?"/>
+        <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
+               label="Compute accessibility profiles for interacting sequences?"/>
+        <param name="intarna_mode" type="select">
+            <option value="H">Heuristic</option>
+            <option value="M">Exact</option>
+            <option value="S">Seed-only</option>
+        </param>
+        <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
+            label="Summarize interactions at loci level?"/>
     </inputs>
 
     <outputs>
         <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>
         <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/>
+        <data format="tabular" name="interactions" from_work_dir="interactions" label="ChiRA interaction summary on ${on_string}">
+            <filter>summarize == True</filter>
+        </data>
     </outputs>
 
     <tests>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="loci" value="loci.counts"/>
             <param name="ref_type" value="split"/>
             <param name="ref_fasta1" value="ref1.fasta"/>
             <param name="ref_fasta2" value="ref2.fasta"/>
             <param name="annot_choice" value="no"/>
             <param name="hybridize" value="true" />
-            <output name="chimeras" file="chimeras" sort="True"/>
-            <output name="singletons" file="singletons" sort="True"/>
+            <param name="summarize" value="true" />
+            <output name="chimeras" file="chimeras"/>
+            <output name="singletons" file="singletons"/>
+            <output name="interactions" file="interactions"/>
         </test>
     </tests>
     <help>