| Previous changeset 1:83108f3c65aa (2022-02-09) Next changeset 3:1770376208c7 (2023-05-30) |
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Commit message:
planemo upload for repository https://github.com/neilswainston/SbmlToSbol commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6 |
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modified:
sbml2sbol.xml |
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added:
config/job_conf.xml config/tool_conf.xml test-data/sbol_lycopene_output2.xml |
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| diff -r 83108f3c65aa -r 9b3279f37e41 config/job_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config/job_conf.xml Mon May 01 01:31:11 2023 +0000 |
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| @@ -0,0 +1,1 @@ + <tool id="sbml2sbol" destination="local" /> |
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| diff -r 83108f3c65aa -r 9b3279f37e41 config/tool_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config/tool_conf.xml Mon May 01 01:31:11 2023 +0000 |
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| @@ -0,0 +1,3 @@ + <section id="sbc-util" name="SynBioCAD Utilities"> + <tool file="synbiocad-galaxy-wrappers/sbml2sbol/sbml2sbol.xml" /> + </section> |
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| diff -r 83108f3c65aa -r 9b3279f37e41 sbml2sbol.xml --- a/sbml2sbol.xml Wed Feb 09 14:42:01 2022 +0000 +++ b/sbml2sbol.xml Mon May 01 01:31:11 2023 +0000 |
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| @@ -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> |
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| diff -r 83108f3c65aa -r 9b3279f37e41 test-data/sbol_lycopene_output2.xml --- /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 |
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| b'@@ -0,0 +1,1794 @@\n+<?xml version="1.0" ?>\n+<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#">\n+ <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_rbs/1">\n+ <sbol:displayId>P21688_30000_rbs</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_30000_rbs"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/1">\n+ <sbol:displayId>P21688_20000_gene</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000704"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>\n+ <sbol:version>1</sbol:version>\n+ <sbol:component>\n+ <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_5_prime_assembly_0/1">\n+ <sbol:access rdf:resource="http://sbols.org/v2#public"/>\n+ <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_5_prime_assembly/1"/>\n+ <sbol:displayId>rxn_3_5_prime_assembly_0</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_5_prime_assembly_0"/>\n+ <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Component>\n+ </sbol:component>\n+ <sbol:component>\n+ <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_rbs_0/1">\n+ <sbol:access rdf:resource="http://sbols.org/v2#public"/>\n+ <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_rbs/1"/>\n+ <sbol:displayId>P21688_20000_rbs_0</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_rbs_0"/>\n+ <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Component>\n+ </sbol:component>\n+ <sbol:component>\n+ <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_cds_0/1">\n+ <sbol:access rdf:resource="http://sbols.org/v2#public"/>\n+ <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_cds/1"/>\n+ <sbol:displayId>P21688_20000_cds_0</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/P21688_20000_cds_0"/>\n+ <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Component>\n+ </sbol:component>\n+ <sbol:component>\n+ <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_3_prime_assembly_0/1">\n+ <sbol:access rdf:resource="http://sbols.org/v2#public"/>\n+ <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_3_prime_assembly/1"/>\n+ <sbol:displayId>rxn_3_3_prime_assembly_0</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_20000_gene/rxn_3_3_prime_assembly_0"/>\n+ <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Component>\n+ '..b'_0</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/P21688_10000_rbs_0"/>\n+ <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Component>\n+ </sbol:component>\n+ <sbol:component>\n+ <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/P21688_10000_cds_0/1">\n+ <sbol:access rdf:resource="http://sbols.org/v2#public"/>\n+ <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_cds/1"/>\n+ <sbol:displayId>P21688_10000_cds_0</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/P21688_10000_cds_0"/>\n+ <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Component>\n+ </sbol:component>\n+ <sbol:component>\n+ <sbol:Component rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/rxn_3_3_prime_assembly_0/1">\n+ <sbol:access rdf:resource="http://sbols.org/v2#public"/>\n+ <sbol:definition rdf:resource="http://liverpool.ac.uk/ComponentDefinition/rxn_3_3_prime_assembly/1"/>\n+ <sbol:displayId>rxn_3_3_prime_assembly_0</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/rxn_3_3_prime_assembly_0"/>\n+ <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:Component>\n+ </sbol:component>\n+ <sbol:sequenceConstraint>\n+ <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/constraint_0/1">\n+ <sbol:displayId>constraint_0</sbol:displayId>\n+ <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/P21688_10000_rbs_0/1"/>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/constraint_0"/>\n+ <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>\n+ <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/rxn_3_5_prime_assembly_0/1"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:SequenceConstraint>\n+ </sbol:sequenceConstraint>\n+ <sbol:sequenceConstraint>\n+ <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/constraint_1/1">\n+ <sbol:displayId>constraint_1</sbol:displayId>\n+ <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/P21688_10000_cds_0/1"/>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/constraint_1"/>\n+ <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>\n+ <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/P21688_10000_rbs_0/1"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:SequenceConstraint>\n+ </sbol:sequenceConstraint>\n+ <sbol:sequenceConstraint>\n+ <sbol:SequenceConstraint rdf:about="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/constraint_2/1">\n+ <sbol:displayId>constraint_2</sbol:displayId>\n+ <sbol:object rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/rxn_3_3_prime_assembly_0/1"/>\n+ <sbol:persistentIdentity rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/constraint_2"/>\n+ <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>\n+ <sbol:subject rdf:resource="http://liverpool.ac.uk/ComponentDefinition/P21688_10000_gene/P21688_10000_cds_0/1"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:SequenceConstraint>\n+ </sbol:sequenceConstraint>\n+ </sbol:ComponentDefinition>\n+</rdf:RDF>\n' |