--- a/sirius_csifingerid.xml	Thu Mar 19 07:30:54 2020 -0400
+++ b/sirius_csifingerid.xml	Thu Jul 02 11:01:45 2020 -0400
@@ -1,5 +1,5 @@
 <tool id="sirius_csifingerid" name="SIRIUS-CSI:FingerID"
-      version="4.0.1+galaxy3" profile="18.01">
+      version="4.0.1+galaxy4" profile="18.01">
     <description>is used to identify metabolites using single and
         tandem mass spectrometry</description>
     <requirements>
@@ -24,6 +24,29 @@
             --schema $schema
             --temp_dir .
 
+            #if $adducts_cond.adducts_selector == 'select':
+                #for $a in $adducts_cond.adducts
+                    --adducts $a
+                #end for
+            #elif $adducts_cond.adducts_selector == 'all':
+                #if $polarity == 'positive':
+                    --adducts [M+H]+
+                    --adducts [M+NH4]+
+                    --adducts [M+Na]+
+                    --adducts [M+K]+
+                    --adducts [M+CH3OH+H]+
+                    --adducts [M+ACN+H]+
+                    --adducts [M+ACN+Na]+
+                    --adducts [M+2ACN+H]+
+                 #elif $polarity == 'negative':
+                    --adducts [M-H]-
+                    --adducts [M+Cl]-
+                    --adducts [M+HCOO]-
+                    --adducts [M+CH3COO]-
+                 #end if
+            #end if
+
+            --rank_filter $rank_filter
     ]]></command>
     <inputs>
         <param name="input" argument="--input_pth" type="data" format="msp"
@@ -76,6 +99,40 @@
         </param>
         <param argument="--minMSMSpeaks" type="integer" min="0" value="0"
                label="Minimum number of MS/MS peaks"/>
+
+        <conditional name="adducts_cond">
+            <param name="adducts_selector" type="select" label="How to handle adducts"
+                   help="Choose whether to include a suspect list">
+                <option value="msp" selected="True">Use adducts defined in MSP file</option>
+                <option value="select" >Select from list of adducts</option>
+                <option value="all" >Use pre-selected adducts for either pos or neg ionisation mode</option>
+            </param>
+            <when value="msp">
+            </when>
+            <when value="select">
+                <param argument="--adducts" label="Select adducts"
+                       type="select" help="" multiple="true" display="checkboxes">
+                    <option value="[M+H]+" selected="True">[M+H]+ 1.007276</option>
+                    <option value="[M+NH4]+">[M+NH4]+ 18.034374</option>
+                    <option value="[M+Na]+">[M+Na]+ 22.989218</option>
+                    <option value="[M+K]+">[M+K]+ 38.963158</option>
+                    <option value="[M+CH3OH+H]+">[M+CH3OH+H]+ 33.033489</option>
+                    <option value="[M+ACN+H]+">[M+ACN+H]+ 42.033823</option>
+                    <option value="[M+ACN+Na]+">[M+ACN+Na]+ 64.015765</option>
+                    <option value="[M+2ACN+H]+">[M+2ACN+H]+ 83.06037</option>
+                    <option value="[M-H]-" >[M-H]- -1.007276</option>
+                    <option value="[M+Cl]-">[M+Cl]- 34.969402</option>
+                    <option value="[M+HCOO]-">[M+HCOO]- 44.99819</option>
+                    <option value="[M+CH3COO]-">[M+CH3COO]- 59.01385</option>
+                </param>
+            </when>
+            <when value="all">
+            </when>
+        </conditional>
+
+        <param argument="--rank_filter" type="integer" value="0"
+               label="Only show the top ranked annotations less than or equal
+                      to this value (default to show all annotations)"/>
     </inputs>
     <outputs>
         <data name="results" format="tsv"
@@ -109,6 +166,17 @@
             <param name="input" value="invalid_adduct.msp" ftype="msp"/>
             <output name="results" file="invalid_adduct_result.tsv"/>
         </test>
+        <test>
+            <!-- Test all adducts  -->
+            <param name="input" value="RP022611.txt" ftype="msp"/>
+            <param name="profile" value="qtof"/>
+            <param name="polarity" value="negative"/>
+            <conditional name="adducts_cond">
+                <param name="adducts_selector" value="all"/>
+            </conditional>
+            <output name="results" file="RP022611_result_all_adducts.tsv"/>
+
+        </test>
     </tests>
     <help>
 ----------------
@@ -118,13 +186,13 @@
 Description
 -----------
 
-| SIRIUS is a java-based software framework for discovering a landscape of
-| de-novo identification of metabolites using single and tandem mass
-| spectrometry. SIRIUS uses isotope pattern analysis for detecting the
-| molecular formula and further analyses the fragmentation pattern of a
-| compound using fragmentation trees. Website:
-| https://bio.informatik.uni-jena.de/software/sirius/
-|
+SIRIUS is a java-based software framework for discovering a landscape of
+de-novo identification of metabolites using single and tandem mass
+spectrometry. SIRIUS uses isotope pattern analysis for detecting the
+molecular formula and further analyses the fragmentation pattern of a
+compound using fragmentation trees. Website:
+https://bio.informatik.uni-jena.de/software/sirius/
+
 
 Parameters
 ----------