--- a/rnacofold.xml	Tue Jul 18 01:47:42 2017 -0400
+++ b/rnacofold.xml	Fri Sep 22 15:56:00 2017 -0400
@@ -28,6 +28,9 @@
             $constraints.constraintLocation.canonicalBPonly
             $constraints.constraintLocation.enforceConstraint                
         #end if
+        #if str($constraints.constraintLocation.constraintSelector) == "inFile" 
+            -C
+        #end if
         $algorithm_options.allpf
         #if len($algorithm_options.concfiles) == 1
             #for $i in $algorithm_options.concfiles
@@ -107,14 +110,16 @@
         <section name="constraints" title="Structure constraints">
                 <conditional name="constraintLocation">
                     <param name="constraintSelector" type="select" label="Constraints">
-                    <!--	<option value="fromInput">The constraints are included in the input file</option> -->
+                      <!--	<option value="fromInput">The constraints are included in the input file</option> -->
                         <option value="fromFile">The constraints are in a seperate file</option>
+                        <option value="inFile">The constraints are in the fasta input file</option>
                         <option value="none" selected="true">Don't use constraints</option>
                     </param>
                     <!-- <when value="fromInput"></when> -->
                     <when value="none"></when>
+                    <when value="inFile"></when>
                     <when value="fromFile">
-                        <param name="constraintsFile" type="data" format="*" label="Constraints file" argument="--constraint"/>
+                        <param name="constraintsFile" type="data" format="txt" label="Constraints file" argument="--constraint"/>
                         <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from he structure constraint" />
                         <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" />
                     </when>
@@ -129,7 +134,7 @@
             <param name="allpf" type="boolean" checked="false" truevalue="--all_pf" falsevalue="" label="Calculate homo-dimers as well as A and B monomers" help="--all_pf"/>
             <param argument="-c" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Concentrations" help="In addition to everything listed under the -a option, read in initial monomer concentrations and compute the expected equilibrium concentrations of the 5 possible species (AB, AA, BB, A, B)."/>
             <repeat name="concfiles" title="A file with initial concentrations for the two sequences" default="0" max="1" help="The table consits of arbitrary many lines with just two numbers (the concentration of sequence A and B). This option will automatically toggle the −c (and thus -a and --all_pf) options">
-                <param type="data" name="concfile" format="*" label="Concentrations file"/>
+                <param type="data" name="concfile" format="txt" label="Concentrations file"/>
             </repeat>			
             <param argument="--pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/>
             <param argument="--bppmThreshold" type="float" value="1e-5" label="Threshold for base pair probabilities" help="By setting the threshold the base pair probabilities that are included in the output can be varied. By default only those exceeding 1e−5 in probability will be shown as squares in the dot plot. Changing the threshold to any other value allows for increase or decrease of data."/>