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planemo upload commit dd818e990b23b010abe4843aaaa7315606b06bd6
author iuc
date Sat, 15 Oct 2022 21:21:15 +0000
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1 <tool id="sbml2sbol" name="SbmlToSbol" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Convert sbml to sbol format</description>
3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">0.1.13</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">sbml2sbol</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 python -m sbml2sbol
12 --input '$sbml_single_input'
13 --outfile '$sbol_outfile'
14 $adv.rbs
15 --max_prot_per_react '$adv.max_prot_per_react'
16 #if $adv.tirs
17 --tirs '$adv.tirs'
18 #end if
19 --pathway_id '$adv.pathway_id'
20 --uniprotID_key '$adv.uniprotID_key'
21 ]]></command>
22 <inputs>
23 <param name="sbml_single_input" type="data" format="sbml" label="Pathway (SBML)" />
24 <section name="adv" title="Advanced Options" expanded="false">
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)"/>
26 <param argument="--max_prot_per_react" type="integer" value="3" min="1" max="20" label="The maximum number of proteins per reaction" />
27 <param argument="--tirs" type="text" optional="true" label="Space separated RBS strength values" />
28 <param argument="--pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" >
29 <validator type="empty_field" message="Pathway ID is required"/>
30 </param>
31 <param argument="--uniprotID_key" type="text" value="selenzy" label="Uniprot ID" >
32 <validator type="empty_field" message="Uniprot ID is required"/>
33 </param>
34 </section>
35 </inputs>
36 <outputs>
37 <data name="sbol_outfile" format="xml" label="${tool.name}: sbol outfile" />
38 </outputs>
39 <tests>
40 <test>
41 <!-- test 1: check if identical outputs are produced with default parameters -->
42 <param name="sbml_single_input" value="lycopene.xml" />
43 <output name="sbol_outfile" file="sbol_lycopene_output.xml" ftype="xml" compare="diff" sort="true"/>
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>
52 </tests>
53 <help><![CDATA[
54 SBML to SBOL
55 ================
56
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).
58
59 Input
60 -----
61
62 Required:
63
64 * **Pathway (SBML)**\ : Pathway file in SBML format.
65
66 Advanced options:
67
68 * **Calculate the RBS strength?**\ : (boolean) Calculate or not the RBS (Ribosome Binding Site) strength (default: True).
69 * **The maximum number of proteins per reaction**\ : (int) The maximum number of proteins per reaction (default: 3).
70 * **Space separated RBS strength values**\ : (int) The RBS (Ribosome Binding Site) strength values (default: None)
71 * **Group ID of the heterologous pathway**\ : (string) Group ID of the heterologous pathway (default: rp_pathway)
72 * **Uniprot ID**\ : (string) Uniprot ID of the heterologous pathway (default: selenzy)
73
74 Output
75 ------
76
77 * **sbol outfile**\ : output (SBOL) file.
78
79 Project Links
80 ------------------
81
82 * `GitHub <https://github.com/neilswainston/SbmlToSbol>`_
83
84 License
85 -------
86
87 * `MIT <https://raw.githubusercontent.com/neilswainston/SbmlToSbol/master/LICENSE>`_
88
89 ]]></help>
90 </tool>