Mercurial > repos > tduigou > sbml2sbol

annotate sbml2sbol.xml @ 0:f0a06f526c7f draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 09 Dec 2021 14:21:48 +0000
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children 83108f3c65aa
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1 <tool id="sbml2sbol" name="SbmlToSbol" version="0.1.12">
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2 <description>Convert sbml to sbol format</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.12">sbml2sbol</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python -m sbml2sbol
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8 --input '$sbml_single_input'
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9 --outfile '$sbol_outfile'
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10 #if str($adv.rbs) == "true"
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11 --rbs True
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12 #else
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13 --rbs False
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14 #end if
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15 --max_prot_per_react '$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 '$adv.uniprotID_key'
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21 ]]></command>
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22 <inputs>
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23 <param name="sbml_single_input" type="data" format="xml" label="Pathway (SBML)" />
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24 <section name="adv" title="Advanced Options" expanded="false">
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25 <param name="rbs" type="boolean" label="Calculate the RBS strength?" checked="true" />
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26 <param name="max_prot_per_react" type="integer" value="3" label="The maximum number of proteins per reaction" />
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27 <param name="tirs" type="text" optional="true" label="Space separated RBS strength values" />
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28 <param name="pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" />
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29 <param name="uniprotID_key" type="text" value="selenzy" label="Uniprot ID" />
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30 </section>
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31 </inputs>
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32 <outputs>
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33 <data name="sbol_outfile" format="xml" label="${tool.name}: sbol outfile" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <!-- test 1: check if identical outputs are produced with default parameters -->
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38 <param name="sbml_single_input" value="lycopene.xml" />
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39 <output name="sbol_outfile" file="sbol_lycopene_output.xml" ftype="xml" compare="diff" sort="true"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 SBML to SBOL
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44 ================
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45
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46 Convert a single or multiple SBML files to SBOL.
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47
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48 Input
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49 -----
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50
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51 Required:
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52
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53 * **input**\ : (string) path to folder(s) containing rpSBML files and/or rpSBML file path(s).
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54
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55 Advanced options:
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56
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57 * **rbs**\ : (boolean) Calculate or not the RBS strength (default: True).
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58 * **max_prot_per_react**\ : (int) The maximum number of proteins per reaction (default: 3).
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59 * **tirs**\ : (int) The RBS strength values (default: None)
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60 * **pathway_id**\ : (string) Group ID of the heterologous pathway (default: rp_pathway)
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61 * **uniprotID_key**\ : (string) Group ID of the heterologous pathway (default: selenzy)
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62
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63 Output
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64 ------
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65
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66 * **outfile**\ : (string) specify output (SBOL) file.
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67
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68 Project Links
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69 ------------------
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70
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71 * `GitHub <https://github.com/neilswainston/SbmlToSbol>`_
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72
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73 Version
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74 ----------
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75 0.1.12
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76
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77 License
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78 -------
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79
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80 * `MIT <https://raw.githubusercontent.com/neilswainston/SbmlToSbol/master/LICENSE>`_
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81
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82 ]]></help>
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83 </tool>