Mercurial > repos > tduigou > get_sbml_model
changeset 0:4797d0b36ff3 draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Tue, 11 Jan 2022 16:17:26 +0000 |
| parents | |
| children | ceffb29b60c9 |
| files | get_sbml_model.xml |
| diffstat | 1 files changed, 102 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_sbml_model.xml Tue Jan 11 16:17:26 2022 +0000 @@ -0,0 +1,102 @@ +<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.1" profile="19.09"> + <description>Pick an SBML model among a list</description> + <requirements> + <requirement type="package" version="7.81.0">curl</requirement> + <requirement type="package" version="1.11">gzip</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz' + | gunzip > '$sbml_model' + ]]></command> + <inputs> + <param name="input" type="select" label="Strain"> + <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option> + <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option> + <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option> + <option value="iCN900">Clostridioides difficile 630 (iCN900)</option> + <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option> + <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option> + <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option> + <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option> + <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option> + <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option> + <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option> + <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option> + <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option> + <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option> + <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option> + <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option> + <option value="Recon3D">Homo sapiens (Recon3D)</option> + <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option> + <option value="RECON1">Homo sapiens (RECON1)</option> + <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option> + <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option> + <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option> + <option value="iMM1415">Mus musculus (iMM1415)</option> + <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option> + <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option> + <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option> + <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option> + <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option> + <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option> + <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option> + <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option> + <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option> + <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option> + <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option> + <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option> + <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option> + <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option> + <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option> + <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option> + <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option> + <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option> + <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option> + <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option> + <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option> + <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option> + <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option> + <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option> + </param> + </inputs> + <outputs> + <data name="sbml_model" format="xml" label="${tool.name} - ${input}" /> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with iML1515 model input --> + <param name="input" value="iML1515" /> + <output name="sbml_model" md5="9bf81d20cab5476700697ded95b716d1"/> + </test> + </tests> + <help><![CDATA[ +Pick SBML Model +================= + +Download the selected SBML model fromg BiGG database. + + +Version +---------- +0.0.1 + + +Authors +------- + +* Joan Hérisson + + +License +------- + +`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ + + +Acknowledgments +--------------- + +* Kenza Bazi-Kabbaj + + ]]></help> +</tool> \ No newline at end of file