Mercurial > repos > tduigou > get_sbml_model
diff get_sbml_model.xml @ 6:9b5947d48192 draft
planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 87a863d4074543870caef1116b8e9be58005dcdd
| author | tduigou |
|---|---|
| date | Mon, 28 Aug 2023 14:24:48 +0000 |
| parents | 80c32f0cb716 |
| children | 8dc4d3964ab5 |
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--- a/get_sbml_model.xml Tue May 30 21:03:04 2023 +0000 +++ b/get_sbml_model.xml Mon Aug 28 14:24:48 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT"> +<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.4" profile="21.09" license="MIT"> <description>Get an SBML model (BiGG)</description> <requirements> <requirement type="package" version="7.81.0">curl</requirement> @@ -7,87 +7,117 @@ <requirement type="package" version="2.29">requests</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz' - | gunzip > '$model'; + #if str($cond_src.from_src) == 'from_bigg' + curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' && + #else + cp '${cond_src.input_file}' '$model' && + #end if python '$__tool_directory__/'get_infos.py '$model' - --hostid '$input' + --hostid '${cond_src.hostid}' --comp '$compartments' --biomass '$biomass' --taxid '$taxid' ]]></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> + <conditional name="cond_src"> + <param name="from_src" type="select" label="Select source"> + <option value="from_bigg" selected="True">Download model from BiGG</option> + <option value="from_history">Select file from the History</option> + </param> + <when value="from_history"> + <param name="hostid" type="text" help="ID of the model"> + <validator type="empty_field" message="An ID is required"/> + </param> + <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/> + </when> + <when value="from_bigg"> + <param name="hostid" 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> + </when> + </conditional> </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)" /> + <data name="model" format="sbml" label="${cond_src.hostid}" /> + <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" /> + <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" /> + <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" /> </outputs> <tests> <test> - <!-- test 1: check if identical outputs are produced with iML1515 model input --> - <param name="input" value="iML1515" /> - <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/> - <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e"/> - <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/> - <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/> + <conditional name="cond_src"> + <param name="from_src" value="from_bigg" /> + <param name="hostid" value="iML1515" /> + </conditional> + <output name="model" md5="9bf81d20cab5476700697ded95b716d1" /> + <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" /> + <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" /> + <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" /> </test> + <test> + <conditional name="cond_src"> + <param name="from_src" value="from_history" /> + <param name="hostid" value="e_coli_core" /> + <param name="input_file" value="e_coli_core.xml" /> + </conditional> + <output name="model" md5="4574760460afe9e1b3388dc15f354706" /> + <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" /> + <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" /> + <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" /> + </test> </tests> <help><![CDATA[ Pick SBML Model ================= -Download the selected SBML model fromg BiGG database. +Download the selected SBML model fromg BiGG database or get statistics from local SBML model. ]]></help> <creator> <organization name="BioRetroSynth" url="https://github.com/brsynth"/>