--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Mar 22 16:10:46 2022 +0000
@@ -0,0 +1,25 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.3.2</token>
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Helge"
+                familyName="Hecht"
+                url="https://github.com/hechth"
+                identifier="0000-0001-6744-996X" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+                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.
+        ]]>
+    </token>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/riassigner.xml	Tue Mar 22 16:10:46 2022 +0000
@@ -0,0 +1,74 @@
+<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy1" profile="19.05">
+    <description>compute retention indices</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
+
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        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>
+        <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'].
+            ]]></help>
+            </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>
+        </param>
+    </inputs>
+
+    <outputs>
+        <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>
+    </tests>
+
+    <help>
+        <![CDATA[
+        @HELP@
+        ]]>
+    </help>
+</tool>