Mercurial > repos > tduigou > rptools_rpfba
comparison rpfba.xml @ 1:5d35eea4f75d draft
planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author | tduigou |
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date | Wed, 16 Nov 2022 14:58:22 +0000 |
parents | 21349603013a |
children | 082cd90e7254 |
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0:21349603013a | 1:5d35eea4f75d |
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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> |