Mercurial > repos > tduigou > get_sbml_model
diff get_sbml_model.xml @ 2:fa893f77dc22 draft
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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--- a/get_sbml_model.xml Mon Apr 03 09:18:22 2023 +0000 +++ b/get_sbml_model.xml Mon Apr 24 14:49:53 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.2" profile="19.09" license="MIT"> +<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT"> <description>Get an SBML model (BiGG)</description> <requirements> <requirement type="package" version="7.81.0">curl</requirement> @@ -8,7 +8,7 @@ <command detect_errors="exit_code"><![CDATA[ curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz' | gunzip > '$model'; - python '$__tool_directory__/'get_infos.py '$model' --comp '$compartments' --biomass '$biomass' + python '$__tool_directory__/'get_infos.py '$model' --hostid '$input' --comp '$compartments' --biomass '$biomass' --taxid '$taxid' ]]></command> <inputs> <param name="input" type="select" label="Strain"> @@ -63,6 +63,7 @@ </inputs> <outputs> <data name="model" format="sbml" label="${input}" /> + <data name="taxid" format="tsv" label="${input} (taxon id)" /> <data name="compartments" format="tsv" label="${input} (compartments)" /> <data name="biomass" format="tsv" label="${input} (biomass reactions)" /> </outputs> @@ -71,7 +72,8 @@ <!-- test 1: check if identical outputs are produced with iML1515 model input --> <param name="input" value="iML1515" /> <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/> - <output name="comp" md5="e93a875a2d8efc10a880ae3ac0018236"/> + <output name="taxid" md5="ec29688652dd49becf7be2a6c2469287"/> + <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/> <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/> </test> </tests> @@ -84,4 +86,13 @@ <creator> <organization name="BioRetroSynth" url="https://github.com/brsynth"/> </creator> + <citations> + <citation type="bibtex"> + @unpublished{get_sbml_model + author = {Joan Hérisson}, + title = {{get_sbml_model}}, + url = {https://github.com/brsynth/}, + } + </citation> + </citations> </tool>