Don't use unsanitized parameters in BWA, Bowtie, and PerM wrappers

tools/sr_mapping/PerM.xml

@@ -6,7 +6,7 @@ PerM
 #if $s.sourceOfRef.refSource == "history":
     $s.sourceOfRef.ref
 #else:
-    $s.sourceOfRef.index.value
+    $s.sourceOfRef.index
 #end if
 #if $s.mate.singleOrPairs == "single":
     $s.mate.reads

tools/sr_mapping/bowtie_color_wrapper.xml

@@ -47,7 +47,7 @@
       --icutoff="None"
      #end if
     #else:
-     --ref=$refGenomeSource.index.value
+     --ref=$refGenomeSource.index
      --indexSettings="None"
      --iautoB="None"
      --ipacked="None"

tools/sr_mapping/bowtie_wrapper.xml

@@ -50,7 +50,7 @@
       --icutoff="None"
      #end if
     #else:
-     --ref=$refGenomeSource.index.value
+     --ref=$refGenomeSource.index
      --indexSettings="None"
      --iautoB="None"
      --ipacked="None"

tools/sr_mapping/bwa_wrapper.xml

@@ -5,7 +5,7 @@
 #if $genomeSource.refGenomeSource == "history":
 --ref=$genomeSource.ownFile
 #else:
---ref=$genomeSource.indices.value
+--ref=$genomeSource.indices
 #end if
 --fastq=$paired.input1
 #if $paired.sPaired == "paired":