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comparison rpfba.xml @ 1:19be43e96154 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba commit c44f1622de870d9c869b65b4605cc8a22c33076a"
author iuc
date Tue, 01 Feb 2022 13:55:41 +0000
parents 12689dfad4d1
children 79094fd479b2
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0:12689dfad4d1 1:19be43e96154
1 <tool id="rpfba" name="Flux balance analysis" version="@TOOL_VERSION@" profile="19.09"> 1 <tool id="rpfba" name="Flux balance analysis" version="@TOOL_VERSION@" profile="19.09">
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="@TOOL_VERSION@">5.11.1</token> 4 <token name="@TOOL_VERSION@">5.12.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
8 </requirements> 8 </requirements>
9 <stdio> 9 <stdio>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 python -m rptools.rpfba '$pathway' '$model' '$compartment_id' '$pathway_with_fba' 14 python -m rptools.rpfba '$pathway' '$model' '$compartment_id' '$pathway_with_fba'
15 #if str($adv.merge) == "true": 15 #if str($adv.merge) == "true":
16 --merge 16 --merge
17 #end if 17 #end if
18 --objective_rxn_id '$input_sim_type.objective_rxn_id' 18 --objective_rxn_id '$objective_rxn_id'
19 --sim '$input_sim_type.sim_type' 19 --sim '$input_sim_type.sim_type'
20 #if str($adv.ignore_orphan_species) == "true": 20 #if str($adv.ignore_orphan_species) == "true":
21 --ignore_orphan_species 21 --ignore_orphan_species
22 #end if 22 #end if
23 --log "error" 23 --log "error"
24 #if str($input_sim_type.sim_type)=="fraction" 24 #if str($input_sim_type.sim_type)=="fba"
25 --biomass_rxn_id '$biomass_rxn_id' 25 --fraction_of 0.0
26 #else
26 --fraction_of '$input_sim_type.fraction_of' 27 --fraction_of '$input_sim_type.fraction_of'
27 #end if 28 #end if
28 #if str($input_sim_type.sim_type)=="pfba"
29 --biomass_rxn_id '$biomass_rxn_id' 29 --biomass_rxn_id '$biomass_rxn_id'
30 --fraction_of '$input_sim_type.fraction_of'
31 #end if
32 #if str($input_sim_type.sim_type)=="fba"
33 --biomass_rxn_id '$biomass_rxn_id'
34 --fraction_of 0.0
35 #end if
36 ]]></command> 30 ]]></command>
37 <inputs> 31 <inputs>
38 <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" /> 32 <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
39 <param name="model" type="data" format="sbml" label="Model (SBML)" /> 33 <param name="model" type="data" format="sbml" label="Model (SBML)" />
40 <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" >
41 <validator type="empty_field" message="A compartment ID is required"/> 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> 42 </param>
43 <conditional name="input_sim_type"> 43 <conditional name="input_sim_type">
44 <param name="sim_type" type="select" label="Constraint based simulation type"> 44 <param name="sim_type" type="select" label="Constraint based simulation type">
45 <option value="fraction" selected="true">Fraction of Reaction</option> 45 <option value="fraction" selected="true">Fraction of Reaction</option>
46 <option value="fba" >FBA</option> 46 <option value="fba" >FBA</option>
47 <option value="pfba">Parsimonious FBA</option> 47 <option value="pfba">Parsimonious FBA</option>
48 </param> 48 </param>
49 <when value="fraction"> 49 <when value="fraction">
50 <param name="fraction_of" type="float" value="0.75" min="0" max="1.0" 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" />
51 <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" >
52 <validator type="empty_field" message="Reaction ID is required"/>
53 </param>
54 </when> 51 </when>
55 <when value="pfba"> 52 <when value="pfba">
56 <param name="fraction_of" type="float" value="0.95" min="0" max="1.0" label="Fraction of the optimum" /> 53 <param name="fraction_of" type="float" value="0.95" min="0" max="1.0" label="Fraction of the optimum" />
57 <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" >
58 <validator type="empty_field" message="Reaction ID is required"/>
59 </param>
60 </when> 54 </when>
61 <when value="fba"> 55 <when value="fba">
62 <param name="objective_rxn_id" type="text" value="rxn_target" label="reaction ID to optimise" >
63 <validator type="empty_field" message="Reaction ID is required"/>
64 </param>
65 </when> 56 </when>
66 </conditional> 57 </conditional>
67 <param name="biomass_rxn_id" type="text" value="biomass" label="biomass reaction ID" >
68 <validator type="empty_field" message="Biomass reaction ID is required"/>
69 </param>
70 <section name="adv" title="Advanced Options" expanded="false"> 58 <section name="adv" title="Advanced Options" expanded="false">
71 <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" />
72 <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" />
73 </section> 61 </section>
74 </inputs> 62 </inputs>
186 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpfba>`_ 174 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpfba>`_
187 175
188 Version 176 Version
189 ---------- 177 ----------
190 178
191 5.11.1 179 5.12.1
192 180
193 Authors 181 Authors
194 ------- 182 -------
195 183
196 * **Melchior du Lac** 184 * **Melchior du Lac**