--- a/frag4feature.xml	Mon Mar 05 09:58:58 2018 -0500
+++ b/frag4feature.xml	Tue Mar 27 05:38:05 2018 -0400
@@ -1,11 +1,11 @@
-<tool id="frag4feature" name="frag4feature" version="0.0.12">
+<tool id="frag4feature" name="frag4feature" version="0.0.13">
     <macros>
         <import>macros.xml</import>
     </macros>
 
     <expand macro="requirements">
         <!-- would ideally have xcms 3.0.0 but not available in bioconda at the point of tool creation-->
-        <requirement type="package" version="1.46.0" >bioconductor-xcms</requirement>
+       <!-- <requirement type="package" version="1.46.0" >bioconductor-xcms</requirement>-->
     </expand>
 
     <description>
@@ -40,6 +40,10 @@
             #if $convert2RawRT_f4f
                 --convert2RawRT
             #end if
+ 	    #if $createDB
+                --createDB
+            #end if
+
             #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
                 --grp_peaklist=$grp_peaklist
             #end if
@@ -64,19 +68,9 @@
         <param name="plim_f4f" type="float" label="plim" value="0" max="1" min="0"
                     help="min purity of precursor to be included"/>
 
-        <conditional name="grp_peaklist_opt">
-            <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
-                <option value="yes" >Provide group peaklist </option>
-                <option value="no" selected="true">Use default grouped peaklist</option>
-            </param>
-            <when value="no">
-            </when>
-            <when value="yes">
-                <param type="data" name="grp_peaklist" label="grouped peaklist"
-                    help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
-                          CAMERA annotations" format="tsv,tabular"/>
-            </when>
-        </conditional>
+        <param name="createDB" type="boolean" checked="true" label="Create SQLite database of spcetra?"/>
+
+        <expand macro="grp_peaklist" />
 
         <expand macro="fileload" />
 
@@ -104,7 +98,7 @@
             </conditional>
             <param name="xset" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
             <param name="pa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.assess_purity.rdata"/>
-            <output name="rag4feature_grouped_msms" value="frag4feature_output.tsv" >
+            <output name="frag4feature_grouped_msms" value="frag4feature_output.tsv" >
             </output>
         </test>
     </tests>