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comparison rpfba.xml @ 3:aa0f22545cfd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Fri, 18 Nov 2022 16:13:23 +0000
parents ef783701afd7
children
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2:ef783701afd7 3:aa0f22545cfd
1 <tool id="rpfba" name="Flux balance analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="rpfba" name="Flux balance analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>for the RetroPath2.0 heterologous pathways</description> 2 <description>for the RetroPath2.0 heterologous pathways</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">5.13.1</token> 5 <token name="@TOOL_VERSION@">6.0.1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
9 </requirements> 9 </requirements>
10 <stdio> 10 <stdio>
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>