--- a/chira_extract.xml	Thu Mar 12 21:03:24 2020 +0000
+++ b/chira_extract.xml	Fri Mar 20 08:56:48 2020 +0000
@@ -25,11 +25,11 @@
         -sc '$score_cutoff'
         -co '$chimeric_overlap'
         #if str($reference.ref_type) == "single":
-            -f1 '$ref_fasta'
+            -f1 '$reference.ref_fasta'
         #else if str($reference.ref_type) == "split":
-            -f1 '$ref_fasta1'
-            -f2 '$ref_fasta2'
-        #end if        
+            -f1 '$reference.ref_fasta1'
+            -f2 '$reference.ref_fasta2'
+        #end if
         $hybridize
         -p "\${GALAXY_SLOTS:-2}"
         -o ./
@@ -62,7 +62,7 @@
             </when>
             <when value="no">
                 <!-- Do nothing -->
-            </when>        
+            </when>
         </conditional>
         <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1"
                help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/>
@@ -88,12 +88,12 @@
         </conditional>
         <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" />
     </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}"/>
     </outputs>
-    
+
     <tests>
         <test expect_num_outputs="2">
             <param name="loci" value="loci.counts"/>
@@ -112,7 +112,7 @@
 
 **What it does**
 
-This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to. 
+This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to.
 
 **Inputs**