Mercurial > repos > tduigou > sbml2sbol
comparison sbml2sbol.xml @ 2:9b3279f37e41 draft
planemo upload for repository https://github.com/neilswainston/SbmlToSbol commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
author | tduigou |
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date | Mon, 01 May 2023 01:31:11 +0000 |
parents | 83108f3c65aa |
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1:83108f3c65aa | 2:9b3279f37e41 |
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1 <tool id="sbml2sbol" name="SbmlToSbol" version="@TOOL_VERSION@" profile="19.09"> | 1 <tool id="sbml2sbol" name="SbmlToSbol" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT"> |
2 <description>Convert sbml to sbol format</description> | 2 <description>Convert sbml to sbol format</description> |
3 <macros> | 3 <macros> |
4 <token name="@VERSION_SUFFIX@">0</token> | |
4 <token name="@TOOL_VERSION@">0.1.13</token> | 5 <token name="@TOOL_VERSION@">0.1.13</token> |
5 </macros> | 6 </macros> |
6 <requirements> | 7 <requirements> |
7 <requirement type="package" version="@TOOL_VERSION@">sbml2sbol</requirement> | 8 <requirement type="package" version="@TOOL_VERSION@">sbml2sbol</requirement> |
8 </requirements> | 9 </requirements> |
9 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
10 python -m sbml2sbol | 11 python -m sbml2sbol |
11 --input '$sbml_single_input' | 12 --input '$sbml_single_input' |
12 --outfile '$sbol_outfile' | 13 --outfile '$sbol_outfile' |
13 #if str($adv.rbs) == "true" | 14 $adv.rbs |
14 --rbs True | |
15 #else | |
16 --rbs False | |
17 #end if | |
18 --max_prot_per_react '$adv.max_prot_per_react' | 15 --max_prot_per_react '$adv.max_prot_per_react' |
19 #if $adv.tirs | 16 #if $adv.tirs |
20 --tirs '$adv.tirs' | 17 --tirs '$adv.tirs' |
21 #end if | 18 #end if |
22 --pathway_id '$adv.pathway_id' | 19 --pathway_id '$adv.pathway_id' |
23 --uniprotID_key '$adv.uniprotID_key' | 20 --uniprotID_key '$adv.uniprotID_key' |
24 ]]></command> | 21 ]]></command> |
25 <inputs> | 22 <inputs> |
26 <param name="sbml_single_input" type="data" format="xml" label="Pathway (SBML)" /> | 23 <param name="sbml_single_input" type="data" format="sbml" label="Pathway (SBML)" /> |
27 <section name="adv" title="Advanced Options" expanded="false"> | 24 <section name="adv" title="Advanced Options" expanded="false"> |
28 <param name="rbs" type="boolean" label="Calculate the RBS strength?" checked="true" /> | 25 <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)"/> |
29 <param name="max_prot_per_react" type="integer" value="3" min="1" max="20" label="The maximum number of proteins per reaction" /> | 26 <param argument="--max_prot_per_react" type="integer" value="3" min="1" max="20" label="The maximum number of proteins per reaction" /> |
30 <param name="tirs" type="text" optional="true" label="Space separated RBS strength values" /> | 27 <param argument="--tirs" type="text" optional="true" label="Space separated RBS strength values" /> |
31 <param name="pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" > | 28 <param argument="--pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" > |
32 <validator type="empty_field" message="Pathway ID is required"/> | 29 <validator type="empty_field" message="Pathway ID is required"/> |
33 </param> | 30 </param> |
34 <param name="uniprotID_key" type="text" value="selenzy" label="Uniprot ID" > | 31 <param argument="--uniprotID_key" type="text" value="selenzy" label="Uniprot ID" > |
35 <validator type="empty_field" message="Uniprot ID is required"/> | 32 <validator type="empty_field" message="Uniprot ID is required"/> |
36 </param> | 33 </param> |
37 </section> | 34 </section> |
38 </inputs> | 35 </inputs> |
39 <outputs> | 36 <outputs> |
43 <test> | 40 <test> |
44 <!-- test 1: check if identical outputs are produced with default parameters --> | 41 <!-- test 1: check if identical outputs are produced with default parameters --> |
45 <param name="sbml_single_input" value="lycopene.xml" /> | 42 <param name="sbml_single_input" value="lycopene.xml" /> |
46 <output name="sbol_outfile" file="sbol_lycopene_output.xml" ftype="xml" compare="diff" sort="true"/> | 43 <output name="sbol_outfile" file="sbol_lycopene_output.xml" ftype="xml" compare="diff" sort="true"/> |
47 </test> | 44 </test> |
45 <test> | |
46 <!-- test 2: check if identical outputs are produced without RBS calculation --> | |
47 <param name="sbml_single_input" value="lycopene.xml" /> | |
48 <param name="rbs" value="--rbs False" /> | |
49 <param name="max_prot_per_react" value="5" /> | |
50 <output name="sbol_outfile" file="sbol_lycopene_output2.xml" ftype="xml" compare="diff" sort="true"/> | |
51 </test> | |
48 </tests> | 52 </tests> |
49 <help><![CDATA[ | 53 <help><![CDATA[ |
50 SBML to SBOL | 54 SBML to SBOL |
51 ================ | 55 ================ |
52 | 56 |
53 Convert a single or multiple SBML files to SBOL. | 57 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). |
54 | 58 |
55 Input | 59 Input |
56 ----- | 60 ----- |
57 | 61 |
58 Required: | 62 Required: |
59 | 63 |
60 * **input**\ : (string) path to folder(s) containing rpSBML files and/or rpSBML file path(s). | 64 * **Pathway (SBML)**\ : Pathway file in SBML format. |
61 | 65 |
62 Advanced options: | 66 Advanced options: |
63 | 67 |
64 * **rbs**\ : (boolean) Calculate or not the RBS strength (default: True). | 68 * **Calculate the RBS strength?**\ : (boolean) Calculate or not the RBS (Ribosome Binding Site) strength (default: True). |
65 * **max_prot_per_react**\ : (int) The maximum number of proteins per reaction (default: 3). | 69 * **The maximum number of proteins per reaction**\ : (int) The maximum number of proteins per reaction (default: 3). |
66 * **tirs**\ : (int) The RBS strength values (default: None) | 70 * **Space separated RBS strength values**\ : (int) The RBS (Ribosome Binding Site) strength values (default: None) |
67 * **pathway_id**\ : (string) Group ID of the heterologous pathway (default: rp_pathway) | 71 * **Group ID of the heterologous pathway**\ : (string) Group ID of the heterologous pathway (default: rp_pathway) |
68 * **uniprotID_key**\ : (string) Group ID of the heterologous pathway (default: selenzy) | 72 * **Uniprot ID**\ : (string) Uniprot ID of the heterologous pathway (default: selenzy) |
69 | 73 |
70 Output | 74 Output |
71 ------ | 75 ------ |
72 | 76 |
73 * **outfile**\ : (string) specify output (SBOL) file. | 77 * **sbol outfile**\ : output (SBOL) file. |
74 | |
75 Project Links | |
76 ------------------ | |
77 | |
78 * `GitHub <https://github.com/neilswainston/SbmlToSbol>`_ | |
79 | |
80 Version | |
81 ---------- | |
82 0.1.13 | |
83 | |
84 License | |
85 ------- | |
86 | |
87 * `MIT <https://raw.githubusercontent.com/neilswainston/SbmlToSbol/master/LICENSE>`_ | |
88 | |
89 ]]></help> | 78 ]]></help> |
79 <creator> | |
80 <organization name="BioRetroSynth" url="https://github.com/brsynth"/> | |
81 </creator> | |
82 <citations> | |
83 <citation type="bibtex"> | |
84 @unpublished{SbmlToSbol | |
85 author = {Neil Swainston}, | |
86 title = {{SbmlToSbol}}, | |
87 url = {https://github.com/neilswainston/SbmlToSbol}, | |
88 } | |
89 </citation> | |
90 </citations> | |
90 </tool> | 91 </tool> |