--- a/qiime2/qiime_cutadapt_trim-single.xml	Wed Jul 17 01:53:11 2019 -0400
+++ b/qiime2/qiime_cutadapt_trim-single.xml	Tue Aug 13 07:40:25 2019 -0400
@@ -13,14 +13,38 @@
 --p-cores=$pcores
 #end if
 
+
+#if '__sq__' in str($padapter):
+  #set $padapter_temp = $padapter.replace('__sq__', "'")
+  #set $padapter = $padapter_temp
+#end if
+
+#if 'X' in str($padapter):
+  #set $padapter_temp = $padapter.replace('X', "$")
+  #set $padapter = $padapter_temp
+#end if
+
 #if str($padapter):
  --p-adapter="$padapter"
 #end if
 
+
+
+
+
+#if '__sq__' in str($pfront):
+  #set $pfront_temp = $pfront.replace('__sq__', "'")
+  #set $pfront = $pfront_temp
+#end if
+
 #if str($pfront):
  --p-front="$pfront"
 #end if
 
+
+
+
+
 #if '__sq__' in str($panywhere):
   #set $panywhere_temp = $panywhere.replace('__sq__', "'")
   #set $panywhere = $panywhere_temp
@@ -31,7 +55,9 @@
 #end if
 
 
-#if $perrorrate:
+
+
+#if str($perrorrate):
  --p-error-rate=$perrorrate
 #end if
 
@@ -39,11 +65,11 @@
  --p-no-indels
 #end if
 
-#if $ptimes:
+#if str($ptimes):
  --p-times=$ptimes
 #end if
 
-#if $poverlap:
+#if str($poverlap):
  --p-overlap=$poverlap
 #end if
 
@@ -55,7 +81,7 @@
  --p-no-match-adapter-wildcards
 #end if
 
-#if $pminimumlength:
+#if str($pminimumlength):
  --p-minimum-length=$pminimumlength
 #end if