--- a/snap_caller.xml	Tue Jul 28 23:21:11 2015 +0200
+++ b/snap_caller.xml	Fri Sep 11 16:25:49 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="read_alignment" name="SNAP Read Alignment" version="0.1.6.1">
+<tool id="read_alignment" name="SNAP Read Alignment" version="0.1.7.0">
   <description>Map sequence reads to a reference genome using SNAP</description>
   <macros>
     <import>toolshed_macros.xml</import>
@@ -18,7 +18,7 @@
 		#end if
 --ofile '$outputfile' --iformat ${i.mode_choose.input.iformat} --oformat $oformat
 --idx-seedsize '$set.seedsize'
---idx-slack '$set.slack' --maxseeds '$set.maxseeds' --maxhits '$set.maxhits' --clipping=$set.clipping --maxdist '$set.maxdist' --confdiff '$set.confdiff' --confadapt '$set.confadpt'
+--idx-slack '$set.slack' --maxseeds '$set.maxseeds' --maxhits '$set.maxhits' --clipping $set.clipping --maxdist '$set.maxdist' --confdiff '$set.confdiff' --confadapt '$set.confadpt'
 		#if $i.mode_choose.input.header:
 --header '${i.mode_choose.input.header}'
 		#end if
@@ -168,9 +168,9 @@
     	<param name="maxseeds" type="integer" value="25" label="maximum seeds per read (default: 25)" help="Number of seeds to use per read (SNAP option -n) when trying to match it to the reference genome; higher numbers will increase the rate of aligned reads and reduce the rate of misalignments, but will reduce performance."/>
 	    <param name="clipping" type="select" label="read clipping (default: from back and front)" help="Specifies from which end of a read low-quality bases should be clipped (SNAP option -Cxx)">
 	      <option value="++">from back and front</option>
-	      <option value="-+">from back only</option>
-	      <option value="+-">from front only</option>
-	      <option value="--">no clipping</option>
+	      <option value="x+">from back only</option>
+	      <option value="+x">from front only</option>
+	      <option value="xx">no clipping</option>
 	    </param>
 	    <param name="selectivity" type="integer" value="1" label="selectivity (default: 1)" help="randomly choose 1/selectivity of the reads to score (SNAP option -S). The tool uses the default of 1 (or a 0 setting) to indicate that all reads should be worked with." />
 	    <param name="filter_output" type="select" label="filter output (default: no filtering)" help="filter output (SNAP option -F for certain classes of reads.">