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fix(tools): get_sbml_model, adjust input
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@guillaume-gricourt
guillaume-gricourt committed Dec 1, 2023
1 parent d4d35d8 commit 9c99b66
Showing 1 changed file with 59 additions and 58 deletions.
117 changes: 59 additions & 58 deletions tools/get_sbml_model/get_sbml_model.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,17 +9,19 @@
</requirements>
<command detect_errors="exit_code"><![CDATA[
#if str($cond_src.from_src) == 'from_bigg'
curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' &&
#set $hostid=$cond_src.host.split("|")[O]
#set $hostname=$cond_src.host.split("|")[1]
curl -o - 'http://bigg.ucsd.edu/static/models/${hostid}.xml.gz' | gunzip > '$model' &&
#else
#set $hostname=$cond_src.host
#end if
echo "listdir:";
ls;
python '$__tool_directory__/'get_infos.py
#if str($cond_src.from_src) == 'from_bigg'
'$model'
#else
'${cond_src.input_file}'
#end if
--hostname '${cond_src.hostid}'
--hostname '${hostname}'
--taxid '$taxid'
--comp '$compartments'
--biomass '$biomass'
Expand All @@ -31,60 +33,60 @@
<option value="from_history">Select file from the History</option>
</param>
<when value="from_history">
<param name="hostid" type="text" label="Model's fullname" help="Model extended name">
<param name="host" type="text" label="Model's fullname" help="Model extended name">
<validator type="empty_field" message="Organism extended name 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 name="host" type="select" label="Strain">
<option value="iCN718i|Acinetobacter baumannii AYE">Acinetobacter baumannii AYE (iCN718)</option>
<option value="iYO844|Bacillus subtilis subsp. subtilis str. 168">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
<option value="iRC1080|Chlamydomonas reinhardtii">Chlamydomonas reinhardtii (iRC1080)</option>
<option value="iCN900|Clostridioides difficile 630">Clostridioides difficile 630 (iCN900)</option>
<option value="iHN637|Clostridium ljungdahlii DSM 13528">Clostridium ljungdahlii DSM 13528 (iHN637)</option>
<option value="iCHOv1_DG44|Cricetulus griseus">Cricetulus griseus (iCHOv1_DG44)</option>
<option value="iCHOv1|Cricetulus griseus">Cricetulus griseus (iCHOv1)</option>
<option value="iAF1260b|Escherichia coli str. K-12 substr. MG1655">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>
<option value="iAF1260|Escherichia coli str. K-12 substr. MG1655">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>
<option value="iML1515|Escherichia coli str. K-12 substr. MG1655" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>
<option value="iJO1366|Escherichia coli str. K-12 substr. MG1655">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>
<option value="iJR904|Escherichia coli str. K-12 substr. MG1655">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>
<option value="e_coli_core|Escherichia coli str. K-12 substr. MG1655">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>
<option value="iAF987|Geobacter metallireducens GS-15">Geobacter metallireducens GS-15 (iAF987)</option>
<option value="iIT341|Helicobacter pylori 26695">Helicobacter pylori 26695 (iIT341)</option>
<option value="iAT_PLT_636|Homo sapiens">Homo sapiens (iAT_PLT_636)</option>
<option value="Recon3D|Homo sapiens">Homo sapiens (Recon3D)</option>
<option value="iAB_RBC_283|Homo sapiens">Homo sapiens (iAB_RBC_283)</option>
<option value="RECON1|Homo sapiens">Homo sapiens (RECON1)</option>
<option value="iYL1228|Klebsiella pneumoniae subsp. pneumoniae MGH 78578">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>
<option value="iNF517|Lactococcus lactis subsp. cremoris MG1363">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>
<option value="iAF692|Methanosarcina barkeri str. Fusaro">Methanosarcina barkeri str. Fusaro (iAF692)</option>
<option value="iMM1415|Mus musculus">Mus musculus (iMM1415)</option>
<option value="iNJ661|Mycobacterium tuberculosis H37Rv">Mycobacterium tuberculosis H37Rv (iNJ661)</option>
<option value="iEK1008|Mycobacterium tuberculosis H37Rv">Mycobacterium tuberculosis H37Rv (iEK1008)</option>
<option value="iLB1027_lipid|Phaeodactylum tricornutum CCAP 1055/1">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>
<option value="iAM_Pb448|Plasmodium berghei">Plasmodium berghei (iAM_Pb448)</option>
<option value="iAM_Pc455|Plasmodium cynomolgi strain B">Plasmodium cynomolgi strain B (iAM_Pc455)</option>
<option value="iAM_Pf480|Plasmodium falciparum 3D7">Plasmodium falciparum 3D7 (iAM_Pf480)</option>
<option value="iAM_Pk459|Plasmodium knowlesi strain H">Plasmodium knowlesi strain H (iAM_Pk459)</option>
<option value="iAM_Pv461|Plasmodium vivax Sal-1">Plasmodium vivax Sal-1 (iAM_Pv461)</option>
<option value="iJN746|Pseudomonas putida KT2440">Pseudomonas putida KT2440 (iJN746)</option>
<option value="iJN1463|Pseudomonas putida KT2440">Pseudomonas putida KT2440 (iJN1463)</option>
<option value="iND750|Saccharomyces cerevisiae S288C">Saccharomyces cerevisiae S288C (iND750)</option>
<option value="iMM904|Saccharomyces cerevisiae S288C">Saccharomyces cerevisiae S288C (iMM904)</option>
<option value="STM_v1_0|Salmonella enterica subsp. enterica serovar Typhimurium str. LT2">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>
<option value="iYS1720|Salmonella pan-reactome">Salmonella pan-reactome (iYS1720)</option>
<option value="iSB619|Staphylococcus aureus subsp. aureus N315">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>
<option value="iYS854|Staphylococcus aureus subsp. aureus USA300_TCH1516">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>
<option value="iJB785|Synechococcus elongatus PCC 7942">Synechococcus elongatus PCC 7942 (iJB785)</option>
<option value="iJN678|Synechocystis sp. PCC 6803">Synechocystis sp. PCC 6803 (iJN678)</option>
<option value="iSynCJ816|Synechocystis sp. PCC 6803">Synechocystis sp. PCC 6803 (iSynCJ816)</option>
<option value="iLJ478|Thermotoga maritima MSB8">Thermotoga maritima MSB8 (iLJ478)</option>
<option value="iIS312|Trypanosoma cruzi Dm28c">Trypanosoma cruzi Dm28c (iIS312)</option>
<option value="iIS312_Trypomastigote|Trypanosoma cruzi Dm28c">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>
<option value="iIS312_Epimastigote|Trypanosoma cruzi Dm28c">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
<option value="iIS312_Amastigote|Trypanosoma cruzi Dm28c">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
</param>
</when>
</conditional>
Expand All @@ -98,19 +100,18 @@
<data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" />
</outputs>
<tests>
<test>
<test expect_num_outputs="4">
<param name="from_src" value="from_bigg" />
<param name="hostid" value="iML1515" />
<param name="host" value="iML1515|Escherichia coli str. K-12 substr. MG1655" />
<output name="model" md5="9bf81d20cab5476700697ded95b716d1" />
<output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
<output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
<output name="biomass" md5="95c0255bd5dd8753c6dde53c0f2958ea" />
</test>
<test>
<test expect_num_outputs="3">
<conditional name="cond_src">
<param name="from_src" value="from_history" />
<param name="hostname" value="Escherichia coli str. K-12 substr. MG1655" />
<param name="hostid" value="e_coli_core" />
<param name="host" value="Escherichia coli str. K-12 substr. MG1655" />
<param name="input_file" value="e_coli_core.xml" />
</conditional>
<output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
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