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comparison physiofit.xml @ 0:198d81ccc75e draft

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planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1
author workflow4metabolomics
date Fri, 28 Oct 2022 10:25:15 +0000
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children 52dddad92226
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-1:000000000000 0:198d81ccc75e
1 <tool id='physiofit' name='PhysioFit' profile='21.09' version='@TOOL_VERSION@+galaxy0' python_template_version='3.5'>
2 <description>Extracellular flux analysis</description>
3 <macros>
4 <token name="@TOOL_VERSION@">2.1.0</token>
5 </macros>
6 <requirements>
7 <requirement type='package' version='@TOOL_VERSION@'>physiofit4galaxy</requirement>
8 </requirements>
9 <command detect_errors='exit_code'><![CDATA[
10
11 physiofit4galaxy --galaxy
12
13 #if $input_selection.input_selector == 'tsv':
14 --data '$input_selection.datafile'
15 #end if
16
17 #if $input_selection.input_selector == 'json':
18 --data '$input_selection.datafile'
19 --config '$input_selection.cfgfile'
20 #end if
21
22
23 #if $basic_settings.lag:
24 -l
25 #end if
26
27 #if $basic_settings.deg_select.deg == 'Yes':
28 -d '$basic_setting.degconsts'
29 #end if
30
31 #if $basic_settings.mc_select.montecarlo == 'Yes':
32 -mc '$basic_settings.mc_select.iters'
33 #end if
34
35 --vini '$advanced_settings.vini'
36
37 #if $advanced_settings.sd_select.sd == 'Yes':
38 -s '$advanced_settings.sd_select.stddevs'
39 #end if
40
41 #if $advanced_settings.cm_select.cm == 'Yes':
42 -cm '$advanced_settings.cm_select.conc_met_bounds'
43 #end if
44
45 #if $advanced_settings.fm_select.fm == 'Yes':
46 -fm '$advanced_settings.fm_select.flux_met_bounds'
47 #end if
48
49 #if $advanced_settings.cb_select.cb == 'Yes':
50 -cb '$advanced_settings.cb_select.conc_biom_bounds'
51 #end if
52
53 #if $advanced_settings.fb_select.fb == 'Yes':
54 -fb '$advanced_settings.fb_select.flux_biom_bounds'
55 #end if
56
57 #if $advanced_settings.verbose:
58 -v
59 #end if
60
61 -op '$plots' -of '$fluxes' -os '$stats' -oc '$config'
62
63 ]]></command>
64 <inputs>
65
66 <conditional name='input_selection'>
67 <param name='input_selector' type='select' label='Choose the input data type to upload (tsv or json config file. For more information please check the documentation'>
68 <option value='tsv'>tsv file</option>
69 <option value='json'>config file (json)</option>
70 </param>
71 <when value='tsv'>
72 <param name='datafile' type='data' format='tabular, txt' multiple='true' label='Upload data file containing biomass and concentration values'/>
73 </when>
74 <when value='json'>
75 <param name='datafile' type='data' format='tabular, txt' multiple='true' label='Upload data file containing biomass and concentration values'/>
76 <param name='cfgfile' type='data' format='json' label='Upload configuration file' />
77 </when>
78 </conditional>
79
80
81 <section name='basic_settings' title='Basic Settings'>
82
83 <param name='lag' type='boolean' argument='--lag' truevalue='-l' falsevalue='' label='Flag to estimate lag phase'/>
84
85 <conditional name='deg_select'>
86 <param name='deg' type='select' label='Select yes to add degradation constants'>
87 <option value='No'>No</option>
88 <option value='Yes'>Yes</option>
89 </param>
90 <when value='Yes'>
91 <param type='text' name='degconsts' value='{}' label='Enter degradation constants in dictionary format (see docs for more information)'/>
92 </when>
93 </conditional>
94
95 <conditional name='mc_select'>
96 <param name='montecarlo' type='select' label='Select yes for sensitivity analysis'>
97 <option value='Yes'>Yes</option>
98 <option value='No'>No</option>
99 </param>
100 <when value='Yes'>
101 <param name='iters' type='integer' value='100' label='Number of iterations for sensitivity analysis'/>
102 </when>
103 </conditional>
104
105 </section>
106
107
108 <section name='advanced_settings' title='Advanced Settings'>
109
110 <param name='vini' type='float' value='1' label='Initial value for fluxes to estimate' />
111
112 <conditional name='sd_select'>
113 <param name='sd' type='select' label='Select yes to add standard deviations'>
114 <option value='No'>No</option>
115 <option value='Yes'>Yes</option>
116 </param>
117 <when value='Yes'>
118 <param name='stddevs' type='text' value='{}' label='Standard deviation on measurements. Give SDs in dictionary format (see docs for more information)' />
119 </when>
120 </conditional>
121
122 <conditional name='cm_select'>
123 <param name='cm' type='select' label='Flag to add bounds on metabolite concentrations'>
124 <option value='No'>No</option>
125 <option value='Yes'>Yes</option>
126 </param>
127 <when value='Yes'>
128 <param name='conc_met_bounds' type='text' value='()' label='Bounds on metabolite concentrations. Bounds should be given in tuple format (see docs for more information)' />
129 </when>
130 </conditional>
131
132 <conditional name='fm_select'>
133 <param name='fm' type='select' label='Select yes to add bounds on metabolite fluxes'>
134 <option value='No'>No</option>
135 <option value='Yes'>Yes</option>
136 </param>
137 <when value='Yes'>
138 <param name='flux_met_bounds' type='text' value='()' label='Bounds on metabolite fluxes. Bounds should be given in tuple format (see docs for more information)' />
139 </when>
140 </conditional>
141
142 <conditional name='cb_select'>
143 <param name='cb' type='select' label='Select yes to add bounds on biomass concentrations'>
144 <option value='No'>No</option>
145 <option value='Yes'>Yes</option>
146 </param>
147 <when value='Yes'>
148 <param name='conc_biom_bounds' type='text' value='()' label='Bounds on biomass concentrations. Bounds should be given in tuple format (see docs for more information)' />
149 </when>
150 </conditional>
151
152 <conditional name='fb_select'>
153 <param name='fb' type='select' label='Select yes to add bounds on biomass fluxes'>
154 <option value='No'>No</option>
155 <option value='Yes'>Yes</option>
156 </param>
157 <when value='Yes'>
158 <param name='flux_biom_bounds' type='text' value='()' label='Bounds on biomass fluxes. Bounds should be given in tuple format (see docs for more information)' />
159 </when>
160 </conditional>
161
162 <param name='verbose' type='boolean' argument='--verbose' truevalue='-v' falsevalue='' label='Flag to get debug information'/>
163
164 </section>
165
166 </inputs>
167
168 <outputs>
169 <data name='plots' label='Plots' format='pdf'/>
170 <data name='fluxes' label='Flux_results' format='tabular'/>
171 <data name='stats' label='Stat_results' format='tabular'/>
172 <data name='config' label='Config_file' format='json'/>
173 </outputs>
174
175 <tests>
176 <test>
177 <param name='input_selection|input_selector' value='tsv' />
178 <param name='input_selection|datafile' value='KEIO_ROBOT6_1.tsv' />
179 <section name='basic_settings'>
180 <param name='lag' value='No'/>
181 <param name='deg_select|deg' value='No'/>
182 <param name='mc_select|montecarlo' value='Yes'/>
183 </section>
184 <section name='advanced_settings'>
185 <param name='vini' value='1'/>
186 <param name='sd_select|sd' value='No'/>
187 <param name='cm_select|cm' value='No'/>
188 <param name='fm_select|fm' value='No'/>
189 <param name='cb_select|cb' value='No'/>
190 <param name='fb_select|fb' value='No'/>
191 <param name='verbose' value='No'/>
192 </section>
193 <output name='fluxes'>
194 <assert_contents>
195 <has_n_columns n='7'/>
196 <has_n_lines n='7'/>
197 <has_size value='767' delta='20'/>
198 </assert_contents>
199 </output>
200 </test>
201 </tests>
202
203 <help><![CDATA[
204 .. class:: warningmark
205
206 **PhysioFit is a scientific tool designed to i) quantify exchange (production and consumption) fluxes and ii) cell growth
207 rate during (batch) cultivations of microorganisms.**
208
209 Fluxes are estimated from time-course measurements of extracellular metabolites and biomass concentrations. PhysioFit has been designed to
210 calculate fluxes in batch experiments, assuming cells are in metabolic (pseudo) steady-state (i.e. fluxes are constant during the experiment).
211
212 **PhysioFit includes the following features:**
213
214 * **calculation of growth rate and extracellular (uptake and production) fluxes**.
215 * if cell growth has some **lag** (e.g. due to adaptation to a novel environment), lag can be taken into account and lag time estimated.
216 * **non-enzymatic degradation** of some metabolites (e.g. DHA or glutamine) can be estimated and taken into account when calculating fluxes.
217 * sensitivity analyses are performed to **estimate the precision of the calculated fluxes**.
218 * **evaluation of the goodness of fit and visual inspection of the fitted curves**.
219 * shipped as a **library** with both a **graphical** and **command line** interface,
220 * open-source, free and easy to install everywhere where Python 3 and pip run,
221 * biologist-friendly.
222
223 It is one of the routine tools that we use at the MetaSys team and `MetaToul platform <http://www.metatoul.fr>`_ to calculate fluxes.
224
225 The code is open-source, and available on `GitHub <https://github.com/MetaSys-LISBP/PhysioFit/>`_ under a GPLv3 license.
226
227 We strongly encourage you to read the `documentation <https://physiofit.readthedocs.io/en/latest/>`_ before using PhysioFit.
228
229 ]]></help>
230 <citations>
231 <citation type='bibtex'>
232 @misc{githubphysiofit,
233 author = {Le Gregam, Loic},
234 year = {2022},
235 title = {PhysioFit},
236 publisher = {Peiro et al.},
237 journal = {Appl Environ Microbiol},
238 url = {https://journals.asm.org/doi/10.1128/AEM.00768-19},
239 }</citation>
240 </citations>
241 </tool>