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comparison get_sbml_model.xml @ 2:fa893f77dc22 draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
author tduigou
date Mon, 24 Apr 2023 14:49:53 +0000
parents ceffb29b60c9
children f59e65c1606a
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1:ceffb29b60c9 2:fa893f77dc22
1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.0.2" profile="19.09" license="MIT"> 1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT">
2 <description>Get an SBML model (BiGG)</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 <requirement type="package" version="5.19.2">python-libsbml</requirement>
7 </requirements> 7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz' 9 curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
10 | gunzip > '$model'; 10 | gunzip > '$model';
11 python '$__tool_directory__/'get_infos.py '$model' --comp '$compartments' --biomass '$biomass' 11 python '$__tool_directory__/'get_infos.py '$model' --hostid '$input' --comp '$compartments' --biomass '$biomass' --taxid '$taxid'
12 ]]></command> 12 ]]></command>
13 <inputs> 13 <inputs>
14 <param name="input" type="select" label="Strain"> 14 <param name="input" type="select" label="Strain">
15 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option> 15 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>
16 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option> 16 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
61 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option> 61 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
62 </param> 62 </param>
63 </inputs> 63 </inputs>
64 <outputs> 64 <outputs>
65 <data name="model" format="sbml" label="${input}" /> 65 <data name="model" format="sbml" label="${input}" />
66 <data name="taxid" format="tsv" label="${input} (taxon id)" />
66 <data name="compartments" format="tsv" label="${input} (compartments)" /> 67 <data name="compartments" format="tsv" label="${input} (compartments)" />
67 <data name="biomass" format="tsv" label="${input} (biomass reactions)" /> 68 <data name="biomass" format="tsv" label="${input} (biomass reactions)" />
68 </outputs> 69 </outputs>
69 <tests> 70 <tests>
70 <test> 71 <test>
71 <!-- test 1: check if identical outputs are produced with iML1515 model input --> 72 <!-- test 1: check if identical outputs are produced with iML1515 model input -->
72 <param name="input" value="iML1515" /> 73 <param name="input" value="iML1515" />
73 <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/> 74 <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>
74 <output name="comp" md5="e93a875a2d8efc10a880ae3ac0018236"/> 75 <output name="taxid" md5="ec29688652dd49becf7be2a6c2469287"/>
76 <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/>
75 <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/> 77 <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>
76 </test> 78 </test>
77 </tests> 79 </tests>
78 <help><![CDATA[ 80 <help><![CDATA[
79 Pick SBML Model 81 Pick SBML Model
82 Download the selected SBML model fromg BiGG database. 84 Download the selected SBML model fromg BiGG database.
83 ]]></help> 85 ]]></help>
84 <creator> 86 <creator>
85 <organization name="BioRetroSynth" url="https://github.com/brsynth"/> 87 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
86 </creator> 88 </creator>
89 <citations>
90 <citation type="bibtex">
91 @unpublished{get_sbml_model
92 author = {Joan Hérisson},
93 title = {{get_sbml_model}},
94 url = {https://github.com/brsynth/},
95 }
96 </citation>
97 </citations>
87 </tool> 98 </tool>