Mercurial > repos > tduigou > sbml2sbol

changeset 2:9b3279f37e41 draft

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planemo upload for repository https://github.com/neilswainston/SbmlToSbol commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
author tduigou
date Mon, 01 May 2023 01:31:11 +0000
parents 83108f3c65aa
children 1770376208c7
files config/job_conf.xml config/tool_conf.xml sbml2sbol.xml test-data/sbol_lycopene_output2.xml
diffstat 4 files changed, 1837 insertions(+), 38 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/job_conf.xml	Mon May 01 01:31:11 2023 +0000
@@ -0,0 +1,1 @@
+    <tool id="sbml2sbol" destination="local" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/tool_conf.xml	Mon May 01 01:31:11 2023 +0000
@@ -0,0 +1,3 @@
+  <section id="sbc-util" name="SynBioCAD Utilities">
+    <tool file="synbiocad-galaxy-wrappers/sbml2sbol/sbml2sbol.xml" />
+  </section>
--- a/sbml2sbol.xml	Wed Feb 09 14:42:01 2022 +0000
+++ b/sbml2sbol.xml	Mon May 01 01:31:11 2023 +0000
@@ -1,6 +1,7 @@
-<tool id="sbml2sbol" name="SbmlToSbol" version="@TOOL_VERSION@" profile="19.09">
+<tool id="sbml2sbol" name="SbmlToSbol" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
     <description>Convert sbml to sbol format</description>
     <macros>
+        <token name="@VERSION_SUFFIX@">0</token>
         <token name="@TOOL_VERSION@">0.1.13</token>
     </macros>
     <requirements>
@@ -8,13 +9,9 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python -m sbml2sbol
-            --input '$sbml_single_input'
-            --outfile '$sbol_outfile'
-        #if str($adv.rbs) == "true"
-            --rbs True
-        #else
-            --rbs False
-        #end if
+        --input '$sbml_single_input'
+        --outfile '$sbol_outfile'
+        $adv.rbs
         --max_prot_per_react '$adv.max_prot_per_react'
         #if $adv.tirs 
             --tirs '$adv.tirs'
@@ -23,15 +20,15 @@
         --uniprotID_key '$adv.uniprotID_key'
     ]]></command>
     <inputs>
-        <param name="sbml_single_input" type="data" format="xml" label="Pathway (SBML)" />
+        <param name="sbml_single_input" type="data" format="sbml" label="Pathway (SBML)" />
         <section name="adv" title="Advanced Options" expanded="false">
-            <param name="rbs" type="boolean" label="Calculate the RBS strength?" checked="true" />
-            <param name="max_prot_per_react" type="integer" value="3" min="1" max="20" label="The maximum number of proteins per reaction" />
-            <param name="tirs" type="text" optional="true" label="Space separated RBS strength values" />
-            <param name="pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" >
+            <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 name="uniprotID_key" type="text" value="selenzy" label="Uniprot ID" >
+            <param argument="--uniprotID_key" type="text" value="selenzy" label="Uniprot ID" >
                 <validator type="empty_field" message="Uniprot ID is required"/>
             </param>
         </section>
@@ -45,46 +42,50 @@
             <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
 ================
 
-Convert a single or multiple SBML files 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:
 
-* **input**\ : (string) path to folder(s) containing rpSBML files and/or rpSBML file path(s).
+* **Pathway (SBML)**\ : Pathway file in SBML format.
 
 Advanced options:
 
-* **rbs**\ : (boolean) Calculate or not the RBS strength (default: True).
-* **max_prot_per_react**\ : (int) The maximum number of proteins per reaction (default: 3).
-* **tirs**\ : (int) The RBS strength values (default: None)
-* **pathway_id**\ : (string) Group ID of the heterologous pathway (default: rp_pathway)
-* **uniprotID_key**\ : (string) Group ID of the heterologous pathway (default: selenzy)
+* **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
 ------
 
-* **outfile**\ : (string) specify output (SBOL) file.
-
-Project Links
-------------------
-
-* `GitHub <https://github.com/neilswainston/SbmlToSbol>`_
-
-Version
-----------
-0.1.13
-
-License
--------
-
-* `MIT <https://raw.githubusercontent.com/neilswainston/SbmlToSbol/master/LICENSE>`_
-
+* **sbol outfile**\ : output (SBOL) file.
     ]]></help>
-</tool>
\ No newline at end of file
+    <creator>
+        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
+    </creator>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{SbmlToSbol
+                author = {Neil Swainston},
+                title = {{SbmlToSbol}},
+                url = {https://github.com/neilswainston/SbmlToSbol},
+            }
+        </citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sbol_lycopene_output2.xml	Mon May 01 01:31:11 2023 +0000
@@ -0,0 +1,1794 @@
+<?xml version="1.0" ?>
+<rdf:RDF xmlns:sys-bio="http://sys-bio.org#" xmlns:sbol="http://sbols.org/v2#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#">
+  <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_rbs/1">
+    <sbol:displayId>P21688_30000_rbs</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_rbs"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:version>1</sbol:version>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/1">
+    <sbol:displayId>P21688_20000_gene</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000704"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
+    <sbol:version>1</sbol:version>
+    <sbol:component>
+      <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_5_prime_assembly_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_5_prime_assembly/1"/>
+        <sbol:displayId>rxn_3_5_prime_assembly_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_5_prime_assembly_0"/>
+        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_rbs_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_rbs/1"/>
+        <sbol:displayId>P21688_20000_rbs_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_rbs_0"/>
+        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_cds_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_cds/1"/>
+        <sbol:displayId>P21688_20000_cds_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_cds_0"/>
+        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_3_prime_assembly_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_3_prime_assembly/1"/>
+        <sbol:displayId>rxn_3_3_prime_assembly_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_3_prime_assembly_0"/>
+        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/constraint_0/1">
+        <sbol:displayId>constraint_0</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_rbs_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/constraint_0"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_5_prime_assembly_0/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/constraint_1/1">
+        <sbol:displayId>constraint_1</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_cds_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/constraint_1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_rbs_0/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/constraint_2/1">
+        <sbol:displayId>constraint_2</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_3_prime_assembly_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/constraint_2"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_cds_0/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_cds/1">
+    <sbol:displayId>P21688_20000_cds</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_cds"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:version>1</sbol:version>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/1">
+    <sbol:displayId>P21688_30000_gene</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000704"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
+    <sbol:version>1</sbol:version>
+    <sbol:component>
+      <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/rxn_3_5_prime_assembly_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_5_prime_assembly/1"/>
+        <sbol:displayId>rxn_3_5_prime_assembly_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/rxn_3_5_prime_assembly_0"/>
+        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_rbs_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_rbs/1"/>
+        <sbol:displayId>P21688_30000_rbs_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_rbs_0"/>
+        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_cds_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_cds/1"/>
+        <sbol:displayId>P21688_30000_cds_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_cds_0"/>
+        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/rxn_3_3_prime_assembly_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_3_prime_assembly/1"/>
+        <sbol:displayId>rxn_3_3_prime_assembly_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/rxn_3_3_prime_assembly_0"/>
+        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/constraint_0/1">
+        <sbol:displayId>constraint_0</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_rbs_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/constraint_0"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/rxn_3_5_prime_assembly_0/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/constraint_1/1">
+        <sbol:displayId>constraint_1</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_cds_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/constraint_1"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_rbs_0/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+    <sbol:sequenceConstraint>
+      <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/constraint_2/1">
+        <sbol:displayId>constraint_2</sbol:displayId>
+        <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/rxn_3_3_prime_assembly_0/1"/>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/constraint_2"/>
+        <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
+        <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_gene/P21688_30000_cds_0/1"/>
+        <sbol:version>1</sbol:version>
+      </sbol:SequenceConstraint>
+    </sbol:sequenceConstraint>
+  </sbol:ComponentDefinition>
+  <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/1">
+    <sbol:displayId>P21683_30000_gene</sbol:displayId>
+    <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene"/>
+    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000704"/>
+    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
+    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
+    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
+    <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
+    <sbol:version>1</sbol:version>
+    <sbol:component>
+      <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/rxn_1_5_prime_assembly_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_1_5_prime_assembly/1"/>
+        <sbol:displayId>rxn_1_5_prime_assembly_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/rxn_1_5_prime_assembly_0"/>
+        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
+      <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/P21683_30000_rbs_0/1">
+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
+        <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_rbs/1"/>
+        <sbol:displayId>P21683_30000_rbs_0</sbol:displayId>
+        <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21683_30000_gene/P21683_30000_rbs_0"/>
+        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
+        <sbol:version>1</sbol:version>
+      </sbol:Component>
+    </sbol:component>
+    <sbol:component>
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+        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
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