Mercurial > repos > tduigou > rptools_rpfba
comparison rpfba.xml @ 1:5d35eea4f75d draft
planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
| author | tduigou |
|---|---|
| date | Wed, 16 Nov 2022 14:58:22 +0000 |
| parents | 21349603013a |
| children | 082cd90e7254 |
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| 0:21349603013a | 1:5d35eea4f75d |
|---|---|
| 65 <data name="pathway_with_fba" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" /> | 65 <data name="pathway_with_fba" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" /> |
| 66 </outputs> | 66 </outputs> |
| 67 <tests> | 67 <tests> |
| 68 <test> | 68 <test> |
| 69 <!-- test 1: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718) --> | 69 <!-- test 1: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718) --> |
| 70 <param name="pathway" value="rp_001_0001.xml" /> | 70 <param name="pathway" value="rp_001_0001_rpfba_in.xml" /> |
| 71 <param name="model" value="iCN718.xml.gz" /> | 71 <param name="model" value="iCN718.xml.gz" /> |
| 72 <param name="biomass_rxn_id" value="R_BIOMASS__3" /> | 72 <param name="biomass_rxn_id" value="R_BIOMASS__3" /> |
| 73 <output name="pathway_with_fba" > | 73 <output name="pathway_with_fba" > |
| 74 <assert_contents> | 74 <assert_contents> |
| 75 <is_valid_xml /> | 75 <is_valid_xml /> |
| 81 </assert_contents> | 81 </assert_contents> |
| 82 </output> | 82 </output> |
| 83 </test> | 83 </test> |
| 84 <test> | 84 <test> |
| 85 <!-- test 2: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718) and sim_type=fba--> | 85 <!-- test 2: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718) and sim_type=fba--> |
| 86 <param name="pathway" value="rp_001_0001.xml" /> | 86 <param name="pathway" value="rp_001_0001_rpfba_in.xml" /> |
| 87 <param name="model" value="iCN718.xml.gz" /> | 87 <param name="model" value="iCN718.xml.gz" /> |
| 88 <param name="biomass_rxn_id" value="R_BIOMASS__3" /> | 88 <param name="biomass_rxn_id" value="R_BIOMASS__3" /> |
| 89 <conditional name="input_sim_type"> | 89 <conditional name="input_sim_type"> |
| 90 <param name="sim_type" value="fba"/> | 90 <param name="sim_type" value="fba"/> |
| 91 </conditional> | 91 </conditional> |
| 99 </assert_contents> | 99 </assert_contents> |
| 100 </output> | 100 </output> |
| 101 </test> | 101 </test> |
| 102 <test> | 102 <test> |
| 103 <!-- test 3: check if identical outputs are produced with R_DM_biomass_c biomass name ID and BiGG model (iCN718) and sim_type=pfba--> | 103 <!-- test 3: check if identical outputs are produced with R_DM_biomass_c biomass name ID and BiGG model (iCN718) and sim_type=pfba--> |
| 104 <param name="pathway" value="rp_001_0001.xml" /> | 104 <param name="pathway" value="rp_001_0001_rpfba_in.xml" /> |
| 105 <param name="model" value="iCN718.xml.gz" /> | 105 <param name="model" value="iCN718.xml.gz" /> |
| 106 <param name="biomass_rxn_id" value="R_DM_biomass_c" /> | 106 <param name="biomass_rxn_id" value="R_DM_biomass_c" /> |
| 107 <conditional name="input_sim_type"> | 107 <conditional name="input_sim_type"> |
| 108 <param name="sim_type" value="pfba"/> | 108 <param name="sim_type" value="pfba"/> |
| 109 </conditional> | 109 </conditional> |