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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 10 Feb 2022 11:36:24 +0000
parents fb5efc456dcc
children 6f0d786299ca
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0:fb5efc456dcc 1:c554f15279fe
1 <tool id="rpFBA" name="FBA" version="5.9.2"> 1 <tool id="rpfba" name="FBA" version="@TOOL_VERSION@" profile="19.09">
2 <description>Perform FBA for the RetroPath2.0 heterologous pathways</description> 2 <description>Perform FBA for the RetroPath2.0 heterologous pathways</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="5.9.2">rptools</requirement> 4 <token name="@TOOL_VERSION@">5.12.1</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
5 </requirements> 8 </requirements>
6 <stdio> 9 <stdio>
7 <regex match="WARNING" level="warning" /> 10 <regex match="WARNING" level="warning" />
8 <regex match="ERROR" level="fatal" /> 11 <regex match="ERROR" level="fatal" />
9 </stdio> 12 </stdio>
10 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
11 python -m rptools.rpfba '$pathway' '$model' '$compartment_id' '$pathway_with_fba' 14 python -m rptools.rpfba '$pathway' '$model' '$compartment_id' '$pathway_with_fba'
12 #if str($adv.merge) == "true": 15 #if str($adv.merge) == "true":
13 --merge 16 --merge
14 #end if 17 #end if
15 --objective_rxn_id '$input_sim_type.objective_rxn_id' 18 --objective_rxn_id '$objective_rxn_id'
16 --sim '$input_sim_type.sim_type' 19 --sim '$input_sim_type.sim_type'
17 #if str($adv.ignore_orphan_species) == "true": 20 #if str($adv.ignore_orphan_species) == "true":
18 --ignore_orphan_species 21 --ignore_orphan_species
19 #end if 22 #end if
20 --log '$adv.log_level' 23 --log "error"
21 #if str($input_sim_type.sim_type)=="fraction" 24 #if str($input_sim_type.sim_type)=="fba"
22 --biomass_rxn_id '$input_sim_type.biomass_rxn_id' 25 --fraction_of 0.0
23 --fraction_of '$input_sim_type.fraction_of' 26 #else
24 #end if 27 --fraction_of '$input_sim_type.fraction_of'
25 #if str($input_sim_type.sim_type)=="pfba" 28 #end if
26 --biomass_rxn_id '' 29 --biomass_rxn_id '$biomass_rxn_id'
27 --fraction_of '$input_sim_type.fraction_of'
28 #end if
29 #if str($input_sim_type.sim_type)=="fba"
30 --biomass_rxn_id ''
31 --fraction_of 0.0
32 #end if
33 ]]></command> 30 ]]></command>
34 <inputs> 31 <inputs>
35 <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" /> 32 <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
36 <param name="model" type="data" format="xml" label="Model (SBML)" /> 33 <param name="model" type="data" format="sbml" label="Model (SBML)" />
37 <param name="compartment_id" type="text" label="SBML compartment ID" value="MNXC3" /> 34 <param name="compartment_id" type="text" label="SBML compartment ID" value="c" >
35 <validator type="empty_field" message="A compartment ID is required"/>
36 </param>
37 <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" >
38 <validator type="empty_field" message="Reaction ID is required"/>
39 </param>
40 <param name="biomass_rxn_id" type="text" label="biomass reaction ID" value="" >
41 <validator type="empty_field" message="Biomass reaction ID is required"/>
42 </param>
38 <conditional name="input_sim_type"> 43 <conditional name="input_sim_type">
39 <param name="sim_type" type="select" label="Constraint based simulation type"> 44 <param name="sim_type" type="select" label="Constraint based simulation type">
40 <option value="fraction" selected="true">Fraction of Reaction</option> 45 <option value="fraction" selected="true">Fraction of Reaction</option>
41 <option value="fba" >FBA</option> 46 <option value="fba" >FBA</option>
42 <option value="pfba">Parsimonious FBA</option> 47 <option value="pfba">Parsimonious FBA</option>
43 </param> 48 </param>
44 <when value="fraction"> 49 <when value="fraction">
45 <param name="fraction_of" type="float" value="0.75" label="Fraction of the optimum" /> 50 <param name="fraction_of" type="float" value="0.75" min="0" max="1.0" label="Fraction of the optimum" />
46 <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" /> 51 </when>
47 <param name="biomass_rxn_id" type="text" value="biomass" label="biomass reaction ID" /> 52 <when value="pfba">
48 </when> 53 <param name="fraction_of" type="float" value="0.95" min="0" max="1.0" label="Fraction of the optimum" />
49 <when value="pfba"> 54 </when>
50 <param name="fraction_of" type="float" value="0.95" label="Fraction of the optimum" /> 55 <when value="fba">
51 <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" /> 56 </when>
52 </when>
53 <when value="fba">
54 <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" />
55 </when>
56 </conditional> 57 </conditional>
57 <section name="adv" title="Advanced Options" expanded="false"> 58 <section name="adv" title="Advanced Options" expanded="false">
58 <param name="merge" type="boolean" label="Output the merged model?" checked="false" display="checkboxes" /> 59 <param name="merge" type="boolean" label="Output the merged model?" checked="false" display="checkboxes" />
59 <param name="ignore_orphan_species" type="boolean" label="Ignore metabolites that are only consumed or produced?" checked="true" /> 60 <param name="ignore_orphan_species" type="boolean" label="Ignore metabolites that are only consumed or produced?" checked="true" />
60 <param name="log_level" type="select" label="Log level"> 61 </section>
61 <option value="debug" >debug</option>
62 <option value="info" >info</option>
63 <option value="warning" >warning</option>
64 <option value="error" selected="true">error</option>
65 <option value="critical" >critical</option>
66 </param>
67 </section>
68 </inputs> 62 </inputs>
69 <outputs> 63 <outputs>
70 <data name="pathway_with_fba" format="xml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" /> 64 <data name="pathway_with_fba" format="sbml" label="${tool.name}(${input_sim_type.sim_type}) - ${pathway.name}" />
71 </outputs> 65 </outputs>
72 <tests> 66 <tests>
73 <test> 67 <test>
74 <!-- test 1: check if identical outputs are produced with default parameters --> 68 <!-- test 1: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718) -->
75 <param name="pathway" value="rp_001_0001.xml" /> 69 <param name="pathway" value="rp_001_0001.xml" />
76 <param name="model" value="e_coli_iML1515.sbml" /> 70 <param name="model" value="iCN718.xml.gz" />
77 <output name="pathway_with_fba" file="rp_001_0001_with_fba.xml" ftype="xml" compare="diff" sort="true"/> 71 <param name="biomass_rxn_id" value="R_BIOMASS__3" />
72 <output name="pathway_with_fba" >
73 <assert_contents>
74 <is_valid_xml />
75 <!--check fba_fraction value-->
76 <has_text text="5.54302" />
77 <!--check fba_biomass value-->
78 <has_text text="1.31359" />
79 <has_n_lines n="408" />
80 </assert_contents>
81 </output>
82 </test>
83 <test>
84 <!-- test 2: check if identical outputs are produced with R_BIOMASS__3 biomass name ID and BiGG model (iCN718) and sim_type=fba-->
85 <param name="pathway" value="rp_001_0001.xml" />
86 <param name="model" value="iCN718.xml.gz" />
87 <param name="biomass_rxn_id" value="R_BIOMASS__3" />
88 <conditional name="input_sim_type">
89 <param name="sim_type" value="fba"/>
90 </conditional>
91 <output name="pathway_with_fba" >
92 <assert_contents>
93 <is_valid_xml />
94 <!--check fba_fba value-->
95 <has_text text="16.47058" />
96 <not_has_text text="fba_fraction" />
97 <has_n_lines n="392" />
98 </assert_contents>
99 </output>
100 </test>
101 <test>
102 <!-- 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 <param name="pathway" value="rp_001_0001.xml" />
104 <param name="model" value="iCN718.xml.gz" />
105 <param name="biomass_rxn_id" value="R_DM_biomass_c" />
106 <conditional name="input_sim_type">
107 <param name="sim_type" value="pfba"/>
108 </conditional>
109 <output name="pathway_with_fba" >
110 <assert_contents>
111 <is_valid_xml />
112 <!--check fba_pfba value-->
113 <has_text text="2623.54248" />
114 <not_has_text text="fba_fraction" />
115 <has_n_lines n="392" />
116 </assert_contents>
117 </output>
78 </test> 118 </test>
79 </tests> 119 </tests>
80 <help><![CDATA[ 120 <help><![CDATA[
81 FBA 121 FBA
82 ===== 122 =====
96 - pathway species has not been found in the model (neither by its ID nor its InChIKey), 136 - pathway species has not been found in the model (neither by its ID nor its InChIKey),
97 - the species is not the target, and 137 - the species is not the target, and
98 - the species is only consumed or produced with the heterologue pathway. 138 - the species is only consumed or produced with the heterologue pathway.
99 139
100 .. image:: https://raw.githubusercontent.com/Galaxy-SynBioCAD/rpFBA/standalone/galaxy/img/rpFBA.png 140 .. image:: https://raw.githubusercontent.com/Galaxy-SynBioCAD/rpFBA/standalone/galaxy/img/rpFBA.png
101 :width: 60 % 141 :width: 60 %
102 :align: center 142 :align: center
103 143
104 | 144 |
105 145
106 The above figure illustrates the steps in the tool's calculation of FBA. The pathway is merged with a GEM SBML model and using the FBC package and CobraPy FBA is performed and the fluxes saved to the SBML file. 146 The above figure illustrates the steps in the tool's calculation of FBA. The pathway is merged with a GEM SBML model and using the FBC package and CobraPy FBA is performed and the fluxes saved to the SBML file.
107 147
134 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpfba>`_ 174 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpfba>`_
135 175
136 Version 176 Version
137 ---------- 177 ----------
138 178
139 5.9.2 179 5.12.1
140 180
141 Authors 181 Authors
142 ------- 182 -------
143 183
144 * **Melchior du Lac** 184 * **Melchior du Lac**
149 189
150 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ 190 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
151 191
152 Acknowledgments 192 Acknowledgments
153 --------------- 193 ---------------
154
155 194
156 * Thomas Duigou 195 * Thomas Duigou
157 ]]></help> 196 ]]></help>
158 <citations> 197 <citations>
159 <citation type="bibtex"> 198 <citation type="doi">10.1186/1752-0509-7-74</citation>
160 @article{hucka2016sbml, 199 <citation type="doi">10.1515/jib-2016-290 </citation>
161 title={SBML Level 3 package: Groups, Version 1 Release 1},
162 author={Hucka, Michael and Smith, Lucian P},
163 journal={Journal of integrative bioinformatics},
164 volume={13},
165 number={3},
166 pages={8--29},
167 year={2016},
168 publisher={De Gruyter}
169 }
170 </citation>
171 <citation type="bibtex">
172 @article{ebrahim2013cobrapy,
173 title={COBRApy: COnstraints-based reconstruction and analysis for python},
174 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
175 journal={BMC systems biology},
176 volume={7},
177 number={1},
178 pages={74},
179 year={2013},
180 publisher={Springer}
181 }
182 </citation>
183 </citations> 200 </citations>
184 </tool> 201 </tool>