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