Mercurial > repos > tduigou > get_sbml_model

comparison get_sbml_model.xml @ 1:e276119e73c8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
author tduigou
date Mon, 24 Apr 2023 13:26:25 +0000
parents fd455add46d5
children 52649039cf3f
comparison
equal deleted inserted replaced
0:fd455add46d5 1:e276119e73c8
1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.0.1" profile="19.09"> 1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT">
2 <description>Pick an SBML model among a list</description> 2 <description>Get an SBML model (BiGG)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="7.81.0">curl</requirement> 4 <requirement type="package" version="7.81.0">curl</requirement>
5 <requirement type="package" version="1.11">gzip</requirement> 5 <requirement type="package" version="1.11">gzip</requirement>
6 <requirement type="package" version="5.19.2">python-libsbml</requirement>
6 </requirements> 7 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz' 9 curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
9 | gunzip > '$sbml_model' 10 | gunzip > '$model';
11 python '$__tool_directory__/'get_infos.py '$model' --comp '$compartments' --biomass '$biomass'
10 ]]></command> 12 ]]></command>
11 <inputs> 13 <inputs>
12 <param name="input" type="select" label="Strain"> 14 <param name="input" type="select" label="Strain">
13 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option> 15 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>
14 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option> 16 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
58 <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option> 60 <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
59 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option> 61 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
60 </param> 62 </param>
61 </inputs> 63 </inputs>
62 <outputs> 64 <outputs>
63 <data name="sbml_model" format="xml" label="${tool.name} - ${input}" /> 65 <data name="model" format="sbml" label="${input}" />
66 <data name="compartments" format="tsv" label="${input} (compartments)" />
67 <data name="biomass" format="tsv" label="${input} (biomass reactions)" />
64 </outputs> 68 </outputs>
65 <tests> 69 <tests>
66 <test> 70 <test>
67 <!-- test 1: check if identical outputs are produced with iML1515 model input --> 71 <!-- test 1: check if identical outputs are produced with iML1515 model input -->
68 <param name="input" value="iML1515" /> 72 <param name="input" value="iML1515" />
69 <output name="sbml_model" md5="9bf81d20cab5476700697ded95b716d1"/> 73 <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>
74 <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/>
75 <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>
70 </test> 76 </test>
71 </tests> 77 </tests>
72 <help><![CDATA[ 78 <help><![CDATA[
73 Pick SBML Model 79 Pick SBML Model
74 ================= 80 =================
75 81
76 Download the selected SBML model fromg BiGG database. 82 Download the selected SBML model fromg BiGG database.
77
78
79 Version
80 ----------
81 0.0.1
82
83
84 Authors
85 -------
86
87 * Joan Hérisson
88
89
90 License
91 -------
92
93 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
94
95
96 Acknowledgments
97 ---------------
98
99 * Kenza Bazi-Kabbaj
100
101 ]]></help> 83 ]]></help>
84 <creator>
85 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
86 </creator>
87 <citations>
88 <citation type="bibtex">
89 @unpublished{get_sbml_model
90 author = {Joan Hérisson},
91 title = {{get_sbml_model}},
92 url = {https://github.com/brsynth/},
93 }
94 </citation>
95 </citations>
102 </tool> 96 </tool>