--- a/kc-align.xml	Tue Mar 17 15:24:15 2020 -0400
+++ b/kc-align.xml	Fri Mar 27 15:00:09 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="kc-align" name="Kc-Align" version="0.1.0" python_template_version="3.5">
+<tool id="kc-align" name="Kc-Align" version="0.1.2" python_template_version="3.5">
     <requirements>
-        <requirement type="package" version="0.5">kcalign</requirement>
-        <requirement type="package" version="2.04">kalign2</requirement>
+        <requirement type="package" version="0.5.8">kcalign</requirement>
+        <requirement type="package" version="3.2.2">kalign3</requirement>
     </requirements>
     <command detect_errors="exit_code">
         <![CDATA[
@@ -16,7 +16,8 @@
     ]]></command>
     <inputs>
         <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
-        <param name="reads" type="data" format="fasta" label="Reads" help="Single or multi-FASTA seqeunces to be aligned with the reference" />
+        <param name="reads" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" />
+        <param name="outname" type="text" value="out" label="Output Prefix" />
         <conditional name="position" >
             <param name="mode" type="select" label="Mode" >
                 <option value="genome">Genome</option>
@@ -24,8 +25,8 @@
                 <option value="mixed">Mixed</option>
             </param>
             <when value="genome" >
-                <param name="start" type="integer" value="0" min="0" label="Start Position" help="The 1-indexed start position of the gene of interest in the reference sequence" />
-                <param name="end" type="integer" value="0" min="0" label="End Position" help="The 1-indexed end position of the gene of interest in the reference sequence" />
+                <param name="start" type="text" value="0" label="Start Position(s)" help="The 1-indexed start position of the gene of interest in the reference sequence (For multi-segmented sequences, input each start site separated by a comma ex: 12562,12591)" />
+                <param name="end" type="text" value="0" label="End Position(s)" help="The 1-indexed end position of the gene of interest in the reference sequence (For multi-segmented sequences, input each end site separated by a comma ex: 12592,13905)" />
             </when>
             <when value="gene" >
             </when>
@@ -34,13 +35,13 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="fasta" format="fasta" from_work_dir="kc-align.fasta" label="out.fasta" />
-        <data name="clustal" format="txt" from_work_dir="kc-align.clustal" label="out.clustal" />
+        <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${outname}.fasta" />
+        <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${outname}.clustal" />
     </outputs>
 <tests>
     <test>
-        <param name="reference" ftype="fasta" value="MN908947.3.fasta" />
-        <param name="reads" ftype="fasta" value="corona.fasta" />
+        <param name="reference" ftype="fasta" value="wuhan_ref.fasta" />
+        <param name="reads" ftype="fasta" value="3.fasta" />
         <param name="mode" value="genome" />
         <param name="start" value="21563" />
         <param name="end" value="25384" />
@@ -58,6 +59,8 @@
 
 Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout.
 
+Kc-Align also has functionality for genes that are are composed of more than one continuous sequence (currently only support for two segments). This can be achieved by entering each segments start coordinate in the Start Position parameter separated by a comma and then doing the same for each segments end coordinate in the End Position parameter (Ex: Start Postion: 12562,12591 End Position: 12592,13905) 
+
 Modes:
 ------
         
@@ -73,7 +76,7 @@
     ]]></help>
     <citations>
         <citation type="bibtex">
-        	@misc{githubkcalign,
+            @misc{githubkcalign,
             author = {Nicholas Keener, Emil Bouvier},
             year = {2020},
             title = {Kc-Align},