--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sbml2sbol.xml	Sat Oct 15 21:21:15 2022 +0000
@@ -0,0 +1,90 @@
+<tool id="sbml2sbol" name="SbmlToSbol" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+    <description>Convert sbml to sbol format</description>
+    <macros>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@TOOL_VERSION@">0.1.13</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">sbml2sbol</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m sbml2sbol
+        --input '$sbml_single_input'
+        --outfile '$sbol_outfile'
+        $adv.rbs
+        --max_prot_per_react '$adv.max_prot_per_react'
+        #if $adv.tirs 
+            --tirs '$adv.tirs'
+        #end if
+        --pathway_id '$adv.pathway_id'
+        --uniprotID_key '$adv.uniprotID_key'
+    ]]></command>
+    <inputs>
+        <param name="sbml_single_input" type="data" format="sbml" label="Pathway (SBML)" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param argument="--rbs" type="boolean" truevalue="--rbs True" falsevalue="--rbs False" label="Calculate the RBS strength?" checked="true" help="Calculate or not the RBS (Ribosome Binding Site) strength (default: True)"/>
+            <param argument="--max_prot_per_react" type="integer" value="3" min="1" max="20" label="The maximum number of proteins per reaction" />
+            <param argument="--tirs" type="text" optional="true" label="Space separated RBS strength values" />
+            <param argument="--pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" >
+                <validator type="empty_field" message="Pathway ID is required"/>
+            </param>
+            <param argument="--uniprotID_key" type="text" value="selenzy" label="Uniprot ID" >
+                <validator type="empty_field" message="Uniprot ID is required"/>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="sbol_outfile" format="xml" label="${tool.name}: sbol outfile" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="sbml_single_input" value="lycopene.xml" />
+            <output name="sbol_outfile" file="sbol_lycopene_output.xml" ftype="xml" compare="diff" sort="true"/>
+        </test>
+        <test>
+        <!-- test 2: check if identical outputs are produced without RBS calculation  -->
+            <param name="sbml_single_input" value="lycopene.xml" />
+            <param name="rbs" value="--rbs False" />
+            <param name="max_prot_per_react" value="5" />
+            <output name="sbol_outfile" file="sbol_lycopene_output2.xml" ftype="xml" compare="diff" sort="true"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+SBML to SBOL
+================
+
+This tool takes a pathway model (encoded in SBML) as input and returns a collection of placeholders for the subsequent design of the synthetic DNA that is required to encode the enzymes defined in the pathway model (encoded in SBOL).
+
+Input
+-----
+
+Required:
+
+* **Pathway (SBML)**\ : Pathway file in SBML format.
+
+Advanced options:
+
+* **Calculate the RBS strength?**\ : (boolean) Calculate or not the RBS (Ribosome Binding Site) strength (default: True).
+* **The maximum number of proteins per reaction**\ : (int) The maximum number of proteins per reaction (default: 3).
+* **Space separated RBS strength values**\ : (int) The RBS (Ribosome Binding Site) strength values (default: None)
+* **Group ID of the heterologous pathway**\ : (string) Group ID of the heterologous pathway (default: rp_pathway)
+* **Uniprot ID**\ : (string) Uniprot ID of the heterologous pathway (default: selenzy)
+
+Output
+------
+
+* **sbol outfile**\ : output (SBOL) file.
+
+Project Links
+------------------
+
+* `GitHub <https://github.com/neilswainston/SbmlToSbol>`_
+
+License
+-------
+
+* `MIT <https://raw.githubusercontent.com/neilswainston/SbmlToSbol/master/LICENSE>`_
+
+    ]]></help>
+</tool>
\ No newline at end of file