Mercurial > repos > tduigou > sbml2sbol

comparison sbml2sbol.xml @ 1:83108f3c65aa draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 09 Feb 2022 14:42:01 +0000
parents f0a06f526c7f
children 9b3279f37e41
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0:f0a06f526c7f 1:83108f3c65aa
1 <tool id="sbml2sbol" name="SbmlToSbol" version="0.1.12"> 1 <tool id="sbml2sbol" name="SbmlToSbol" version="@TOOL_VERSION@" profile="19.09">
2 <description>Convert sbml to sbol format</description> 2 <description>Convert sbml to sbol format</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.1.13</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="0.1.12">sbml2sbol</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">sbml2sbol</requirement>
5 </requirements> 8 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
7 python -m sbml2sbol 10 python -m sbml2sbol
8 --input '$sbml_single_input' 11 --input '$sbml_single_input'
9 --outfile '$sbol_outfile' 12 --outfile '$sbol_outfile'
12 #else 15 #else
13 --rbs False 16 --rbs False
14 #end if 17 #end if
15 --max_prot_per_react '$adv.max_prot_per_react' 18 --max_prot_per_react '$adv.max_prot_per_react'
16 #if $adv.tirs 19 #if $adv.tirs
17 --tirs $adv.tirs 20 --tirs '$adv.tirs'
18 #end if 21 #end if
19 --pathway_id '$adv.pathway_id' 22 --pathway_id '$adv.pathway_id'
20 --uniprotID_key '$adv.uniprotID_key' 23 --uniprotID_key '$adv.uniprotID_key'
21 ]]></command> 24 ]]></command>
22 <inputs> 25 <inputs>
23 <param name="sbml_single_input" type="data" format="xml" label="Pathway (SBML)" /> 26 <param name="sbml_single_input" type="data" format="xml" label="Pathway (SBML)" />
24 <section name="adv" title="Advanced Options" expanded="false"> 27 <section name="adv" title="Advanced Options" expanded="false">
25 <param name="rbs" type="boolean" label="Calculate the RBS strength?" checked="true" /> 28 <param name="rbs" type="boolean" label="Calculate the RBS strength?" checked="true" />
26 <param name="max_prot_per_react" type="integer" value="3" label="The maximum number of proteins per reaction" /> 29 <param name="max_prot_per_react" type="integer" value="3" min="1" max="20" label="The maximum number of proteins per reaction" />
27 <param name="tirs" type="text" optional="true" label="Space separated RBS strength values" /> 30 <param name="tirs" type="text" optional="true" label="Space separated RBS strength values" />
28 <param name="pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" /> 31 <param name="pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" >
29 <param name="uniprotID_key" type="text" value="selenzy" label="Uniprot ID" /> 32 <validator type="empty_field" message="Pathway ID is required"/>
33 </param>
34 <param name="uniprotID_key" type="text" value="selenzy" label="Uniprot ID" >
35 <validator type="empty_field" message="Uniprot ID is required"/>
36 </param>
30 </section> 37 </section>
31 </inputs> 38 </inputs>
32 <outputs> 39 <outputs>
33 <data name="sbol_outfile" format="xml" label="${tool.name}: sbol outfile" /> 40 <data name="sbol_outfile" format="xml" label="${tool.name}: sbol outfile" />
34 </outputs> 41 </outputs>
70 77
71 * `GitHub <https://github.com/neilswainston/SbmlToSbol>`_ 78 * `GitHub <https://github.com/neilswainston/SbmlToSbol>`_
72 79
73 Version 80 Version
74 ---------- 81 ----------
75 0.1.12 82 0.1.13
76 83
77 License 84 License
78 ------- 85 -------
79 86
80 * `MIT <https://raw.githubusercontent.com/neilswainston/SbmlToSbol/master/LICENSE>`_ 87 * `MIT <https://raw.githubusercontent.com/neilswainston/SbmlToSbol/master/LICENSE>`_