physiofit: physiofit.xml annotate

annotate physiofit.xml @ 0:198d81ccc75e draft

planemo upload for repository https://github.com/MetaSys-LISBP/PhysioFit commit 188d100128db10dde9bac0bb6c6c60e6946508a1

author	workflow4metabolomics
date	Fri, 28 Oct 2022 10:25:15 +0000
parents
children	52dddad92226

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

Mercurial > repos > workflow4metabolomics > physiofit

annotate physiofit.xml @ 0:198d81ccc75e draft