--- a/combineAnnotations.xml	Thu Dec 05 07:47:31 2019 -0500
+++ b/combineAnnotations.xml	Wed Apr 01 11:21:11 2020 -0400
@@ -9,7 +9,11 @@
             --sm_resultPth='$sm_resultPth'
             --metfrag_resultPth='$metfrag_resultPth'
             --sirius_csi_resultPth='$sirius_csi_resultPth'
-            --probmetab_resultPth='$probmetab_resultPth'
+
+            #if $probmetabCond.probmetabChoice == 'probmetab'
+               --probmetab_resultPth='$probmetabCond.probmetab_resultPth'
+            #end if
+
             --ms1_lookup_resultPth='$ms1_lookup_resultPth'
 
             #if $ms1_lookup_checkAdducts:
@@ -25,8 +29,8 @@
             --probmetab_weight=$probmetab_weight
             --ms1_lookup_weight=$ms1_lookup_weight
             --biosim_weight=$biosim_weight
-
-
+                  
+            
             #if $create_new_database:
               --create_new_database
             #end if
@@ -37,6 +41,10 @@
               --compoundDbPth='$compoundDbTypeCond.compoundDbPth'
             #end if
 
+            #if $summaryOutput:
+              --summaryOutput
+            #end if
+
 
     ]]></command>
     <inputs>
@@ -48,8 +56,19 @@
                help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID)"/>
       <param argument="--sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular"   optional="true"
              help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID)"/>
-      <param argument="--probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular"   optional="true"
-               help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID)"/>
+      <conditional name="probmetabCond">
+            <param name="probmetabChoice" type="select" label="Use probmetab data" help="The result of the Probmetab analysis" >
+                <option value="no_probmetab" selected="true" >Do not include probmetab results</option>
+                <option value="probmetab" >Include probmetab results</option>
+            </param>
+            <when value="probmetab">
+               <param argument="--probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular"   optional="true"
+               help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID). Alternatively any ms1 annotation tool can be used
+                     instead of probmetab"/>
+            </when>
+            <when value="no_probmetab">
+            </when>
+      </conditional>       
       <param argument="--ms1_lookup_resultPth" type="data" label="MS1 Lookup result" format="tsv,tabular"   optional="true"
              help="The result of the a generic MS1 lookup annotation software (e.g. BEAMS can be used)"/>
       <param argument="--ms1_lookup_keepAdducts" type="text" label="MS1 lookup adducts to keep" optional="true"
@@ -67,6 +86,7 @@
       <param argument="--probmetab_weight" type="float" min="0.0" max="1.0" value="0.0" label="Probmetab weight" help="all weights need to sum to 1" />
       <param argument="--ms1_lookup_weight" type="float" min="0.0" max="1.0" value="0.05" label="MS1 Lookup weight" help="all weights need to sum to 1" />
       <param argument="--biosim_weight" type="float" min="0.0" max="1.0" value="0.25" label="Biological similarity weight" help="all weights need to sum to 1" />
+      <param argument="--summaryOutput" type="boolean" checked="true" label="Create summary output" help="Create tab separated file of all annotations and features"/>
       <param argument="--create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
                help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy.
                      When False, the input SQLite database will be updated the results. Use False
@@ -93,8 +113,8 @@
         <test>
             <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" />
             <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
-            <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
-            <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" />
+	    <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
+             <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
             <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" />
             <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
             <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" />