--- a/macros.xml	Fri Aug 20 12:27:54 2021 +0000
+++ b/macros.xml	Sat Sep 04 14:03:58 2021 +0000
@@ -1,10 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.2.0</token>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="0.2.0">riassigner</requirement>
-        </requirements>
-    </xml>
+    <token name="@TOOL_VERSION@">0.3.0</token>
     <xml name="creator">
         <creator>
             <organization
@@ -12,7 +7,6 @@
                 name="RECETOX MUNI" />
         </creator>
     </xml>
-
     <token name="@HELP@">
         <![CDATA[
         RIAssigner can be used to read data from .msp, .csv and .tsv files using matchms and pandas and to compute the retention indices for the data. A reference list of retention indexed compounds (traditionally an Alkane series) with retention times is used to compute the RI for a query dataset of retention time values using the van den Dool method or by using cubic spline based interpolation.

--- a/riassigner.xml	Fri Aug 20 12:27:54 2021 +0000
+++ b/riassigner.xml	Sat Sep 04 14:03:58 2021 +0000
@@ -1,56 +1,63 @@
-<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy0" profile="19.05">
     <description>compute retention indices</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement>
+    </requirements>
     <expand macro="creator"/>
-    <expand macro="requirements" />
 
     <command detect_errors="exit_code"><![CDATA[
-        sh ${symlink_inputs} &&
-        python -m RIAssigner --reference "$reference.element_identifier" --query "$query.element_identifier" --method "$method" --output "output.${query.ext}" &&
-        cp -r 'output.${query.ext}' '${output}'
-    ]]></command>
-
-    <configfiles>
-        <configfile name="symlink_inputs">
-            ln -s '${query}' '${query.element_identifier}'
-            ln -s '${reference}' '${reference.element_identifier}'
-        </configfile>
-    </configfiles>
+        python -m RIAssigner --reference "$reference_section.reference" "$reference_section.reference.ext" "$reference_section.reference_rt_units" --query "$query_section.query" "$query_section.query.ext" "$query_section.query_rt_units" --method "$method" --output "output.${query_section.query.ext}" &&
+        cp -r 'output.${query_section.query.ext}' '${output}'
+        ]]>
+    </command>
 
     <inputs>
-        <param name="reference" type="data" format="csv,tsv,msp">
-            <label>Reference compound list</label>
-            <help><![CDATA[
-            A list of retention time and retention index pairs.
-            Expected columns for RT (oneof): ['rt', 'retention_time'].
-            Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index'].
-            Retention time is expected to be in seconds.
-            ]]></help>
-        </param>
-        <param name="query" type="data" format="csv,tsv,msp">
-            <label>Query compound list</label>
-            <help><![CDATA[
+        <section name="query_section" title="Query dataset" expanded="true">
+            <param name="query" type="data" format="csv,tsv,msp">
+                <label>Query compound list</label>
+                <help><![CDATA[
             A list of compounds with retention times for which to compute the retention index.
             Expected columns for RT (oneof): ['rt', 'retention_time'].
-            Retention time is expected to be in seconds.
             ]]></help>
-        </param>
+            </param>
+            <param name="query_rt_units" type="select" display="radio" help="Retention time units in the query file.">
+                <option value="seconds" selected="true">Seconds</option>
+                <option value="min">Minutes</option>
+            </param>
+        </section>
+        <section name="reference_section" title="Reference dataset" expanded="true">
+            <param name="reference" type="data" format="csv,tsv,msp">
+                <label>Reference compound list</label>
+                <help><![CDATA[
+                A list of retention time and retention index pairs.
+                Expected columns for RT (oneof): ['rt', 'retention_time'].
+                Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index'].
+                ]]></help>
+            </param>
+            <param name="reference_rt_units" type="select" display="radio" help="Retention time units in the reference file.">
+                <option value="seconds" selected="true">Seconds</option>
+                <option value="min">Minutes</option>
+            </param>
+        </section>
         <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use.">
             <option value="kovats" selected="true">Kovats</option>
-            <!-- <option value="cubicspline">CubicSpline </option> -->
+            <option value="cubicspline">CubicSpline </option>
         </param>
     </inputs>
 
     <outputs>
-        <data label="RI using $method of ${query.element_identifier}" name="output" format_source="query" />
+        <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query" metadata_source="query"/>
     </outputs>
 
     <tests>
         <test>
             <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv" />
+            <param name="query_rt_units" value="seconds" />
             <param name="reference" value="Alkanes_20210325.csv" ftype="csv" />
+            <param name="reference_rt_units" value="seconds" />
             <param name="method" value="kovats" />
             <output name="output" file="results.csv" ftype="csv"/>
         </test>