Mercurial > repos > workflow4metabolomics > influx_si
view influx_si.xml @ 2:57f199aa07e4 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit 77b389c6f38fb8eb7d46366e7dd75b01229cc911
| author | workflow4metabolomics |
|---|---|
| date | Wed, 13 Dec 2023 08:56:04 +0000 |
| parents | 4e3d4318113b |
| children |
line wrap: on
line source
<tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy1" profile="21.09"> <description> Estimate metabolic fluxes and concentrations by fitting simulated labeling in metabolites to NMR/MS measurements </description> <creator> <person givenName="Serguei" familyName="Sokol" email="sokol@insa-toulouse.fr" url="https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/cellule-mathematiques/" /> <organization name="INRAE" url="https://www.inrae.fr/" /> <organization name="TBI" url="https://www.toulouse-biotechnology-institute.fr/" /> <organization name="Mathematics Cell" url="https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/cellule-mathematiques/" /> <organization name="MetaToul-FluxoMet" url="https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/metatoul/" /> <organization name="MetaboHub2" url="https://www.metabohub.fr/" /> </creator> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">influx_si</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #for $inp in $input_main: unzip $inp; #end for ret=0; influx_$si.s_i $noopt $noscale $fullsys $emu $irand $ln $sln $tikhreg $lim $ffguess $nocalc $addnoise $TIMEIT $prof #if $opt.meth: --meth='$opt.meth' #end if #if $opt.sens: --sens='$opt.sens' #end if #if $opt.cupx: --cupx='$opt.cupx' #end if #if $opt.cupn: --cupn='$opt.cupn' #end if #if $opt.cupp: --cupp='$opt.cupp' #end if #if $opt.clownr: --clownr='$opt.clownr' #end if #if $opt.cinout: --cinout='$opt.cinout' #end if #if $opt.clowp: --clowp='$opt.clowp' #end if #if $opt.np: --np='$opt.np' #end if #if $opt.zc: --zc='$opt.zc' #end if #if $opt.fseries: --fseries='$opt.fseries' #end if #if $opt.iseries: --iseries='$opt.iseries' #end if #if $opt.seed: --seed='$opt.seed' #end if #if $opt.excl_outliers: --excl_outliers $opt.excl_outliers #end if #if $opt.tblimit: --tblimit='$opt.tblimit' #end if #if $si.s_i == 'i' and $si.time_order != 'None': --time_order='$si.time_order' #end if #for $inp in $input_main: #set base = $inp.name[:-4] --prefix "$base" #end for #if $opt.mtf: --mtf '$opt.mtf' #end if || ret=\$?; #for $inp in $input_main: #set base = $inp.name[:-4] for f in "$base"_res/*.{err,log}; do mv -f "\$f" "\$f".txt || true; done; for f in "$base"_res/*.{sim,stat}; do mv -f "\$f" "\$f".tsv || true; done; for f in "$base"_res/*.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done; rm -rf "$base"_res/tmp || true; #end for exit \$ret; ]]></command> <inputs> <param type="data" format="zip" name="input_main" multiple="true" label="At least one MTF collection (.netw, .miso, ...)"/> <conditional name="si"> <param name="s_i" type="select" label="labeling type" display="radio"> <option value="s">stationary</option> <option value="i">instationary</option> </param> <when value="s"/> <when value="i"> <param argument="--time_order" type="select" display="radio" label="Time order for ODE solving" help="Order 2 is more precise but more time consuming than order 1. The value '1,2' makes to start solving the ODE with the first order scheme then continues with the order 2."> <option value="None">From .opt file or Default</option> <option value="1">1 (Default)</option> <option value="2">2</option> <option value="1,2">1,2</option> </param> </when> </conditional> <section name="opt" title="Advanced Options" expanded="false"> <param argument="--noopt" type="boolean" checked="false" truevalue="--noopt" falsevalue="" label="--noopt" help="no optimization, just use free parameters as is (after a projection on feasibility domain), to calculate dependent fluxes, cumomers, stats and so on" /> <param argument="--noscale" type="boolean" checked="false" truevalue="--noscale" falsevalue="" label="--noscale" help="no scaling factors to optimize => all scaling factors are assumed to be 1" /> <param argument="--fullsys" type="boolean" checked="false" truevalue="--fullsys" falsevalue="" label="--fullsys" help="calculate all cumomer set (not just the reduced one necessary to simulate measurements)" /> <param argument="--emu" type="boolean" checked="false" truevalue="--emu" falsevalue="" label="--emu" help="simulate labeling in EMU approach" /> <param argument="--irand" type="boolean" checked="false" truevalue="--irand" falsevalue="" label="--irand" help="ignore initial approximation for free parameters (free fluxes and metabolite concentrations) from the FTBL file or from a dedicated file (cf --fseries and --iseries option) and use random values drawn uniformly from [0,1] interval" /> <param argument="--ln" type="boolean" checked="false" truevalue="--ln" falsevalue="" label="--ln" help="Least norm solution is used for increments during the non-linear iterations when Jacobian is rank deficient" /> <param argument="--sln" type="boolean" checked="false" truevalue="--sln" falsevalue="" label="--sln" help="Least norm of the solution of linearized problem (and not just of increments) is used when Jacobian is rank deficient" /> <param argument="--tikhreg" type="boolean" checked="false" truevalue="--tikhreg" falsevalue="" label="--tikhreg" help="Approximate least norm solution is used for increments during the non-linear iterations when Jacobian is rank deficient" /> <param argument="--lim" type="boolean" checked="false" truevalue="--lim" falsevalue="" label="--lim" help="The same as --ln but with a function limSolve::lsei()" /> <param argument="--ffguess" type="boolean" checked="false" truevalue="--ffguess" falsevalue="" label="--ffguess" help="Don't use free/dependent flux definitions from FTBL file(s). Make an automatic guess." /> <param argument="--nocalc" type="boolean" checked="false" truevalue="--nocalc" falsevalue="" label="--nocalc" help="generate an R code but not execute it." /> <param argument="--addnoise" type="boolean" checked="false" truevalue="--addnoise" falsevalue="" label="--addnoise" help="Add centered gaussian noise to simulated measurements written to _res.kvh file. SD of this noise is taken from FTBL file" /> <param argument="--TIMEIT" type="boolean" checked="false" truevalue="--TIMEIT" falsevalue="" label="--TIMEIT" help="developer option: measure cpu time or not" /> <param argument="--prof" type="boolean" checked="false" truevalue="--prof" falsevalue="" label="--prof" help="developer option: do time profiling or not" /> <param argument="--meth" type="select" label="--meth" optional="true" help="method for optimization, one of nlsic|BFGS|Nelder-Mead|pso. Default: nlsic"> <option value="BFGS">BFGS</option> <option value="Nelder-Mead">Nelder-Mead</option> <option value="nlsic">nlsic</option> <option value="pso">pso</option> </param> <param argument="--sens" type="text" value="" label="--sens" optional="true" help="sensitivity method: SENS can be 'mc[=N]', mc stands for Monte-Carlo. N is an optional number of Monte-Carlo simulations. Default for N: 10" /> <param argument="--cupx" type="float" min="0" max="1" value="" label="--cupx" optional="true" help="upper limit for reverse fluxes. Must be in interval [0, 1]. Default: 0.999" /> <param argument="--cupn" type="float" min="0" value="" label="--cupn" optional="true" help="absolute limit for net fluxes: -cupn <= netflux <= cupn. Must be non negative. Value 0 means no limit. Default: 1.e3" /> <param argument="--cupp" type="float" min="0" value="" label="--cupp" optional="true" help="upper limit for metabolite pool. Default: 1.e5" /> <param argument="--clownr" type="float" min="0" value="" label="--clownr" optional="true" help="lower limit for not reversible free and dependent fluxes. Zero value (default) means no lower limit" /> <param argument="--cinout" type="float" min="0" value="" label="--cinout" optional="true" help="lower limit for input/output free and dependent fluxes. Must be non negative. Default: 0" /> <param argument="--clowp" type="float" min="0" value="" label="--clowp" optional="true" help="lower limit for free metabolite pools. Must be positive. Default 1.e-8" /> <param argument="--np" type="float" min="0" value="" label="--np" optional="true" help="When integer >= 1, it is a number of parallel subprocesses used in Monte-Carlo (MC) simulations or for multiple FTBL inputs. When NP is a float number between 0 and 1, it gives a fraction of available cores (rounded to closest integer) to be used. Without this option or for NP=0, all available cores in a given node are used for MC simulations." /> <param argument="--zc" type="float" min="0" value="" label="--zc" optional="true" help="Apply zero crossing strategy with non negative threshold for net fluxes" /> <param argument="--fseries" type="text" value="" label="--fseries" optional="true" help="File name with free parameter values for multiple starting points. Default: '' (empty, i.e. only one starting point from the FTBL file is used)" /> <param argument="--iseries" type="text" value="" label="--iseries" optional="true" help="Indexes of starting points to use. Format: '1:10' -- use only first ten starting points; '1,3' -- use the the first and third starting points; '1:10,15,91:100' -- a mix of both formats is allowed. Default: '' (empty, i.e. all provided starting points are used)" /> <param argument="--seed" type="integer" min="0" value="" label="--seed" optional="true" help="Integer (preferably a prime integer) used for reproducible random number generating. It makes reproducible random starting points (--irand) but also Monte-Carlo simulations for sensitivity analysis. Default: none, i.e. current system value is used, so random drawing will be varying at each run." /> <param argument="--excl_outliers" type="float" min="0" max="1" value="" label="--excl_outliers" optional="true" help="This option takes an optional argument, a p-value between 0 and 1 which is used to filter out measurement outliers. The filtering is based on Z statistics calculated on reduced residual distribution. Default: 0.01." /> <param argument="--tblimit" type="integer" min="0" value="0" label="--tblimit" optional="true" help="developer option: set trace back limit for python error messages" /> <param argument="--mtf" type="text" value="" label="--mtf MTF" optional="true" help="MTF is a coma separated list of files with following extensions: netw, linp, miso, mflux, mmet, tvar, cnstr, ftbl, vmtf. Only first 3 files are necessary to obtain a workable FTBL file, others are optional."/> </section> </inputs> <outputs> <collection name="influx_si_output" type="list:list" label="influx_${si.s_i}_on_${on_string}"> <discover_datasets match_relative_path="true" recurse="true" pattern="(?P<identifier_0>[^/]+)_res/(?P<identifier_1>[^/]+)\.(?P<ext>[^.]+)" visible="false"/> </collection> </outputs> <tests> <test> <param name="input_main" value="e_coli.zip" /> <conditional name="si"> <param name="s_i" value="s" /> </conditional> <output_collection name="influx_si_output" type="list:list" count="1"> <element name="e_coli" count="7"> <element name="e_coli.log"> <assert_contents> <has_n_lines n="38"/> <has_line_matching expression="^end.*"/> </assert_contents> </element> </element> </output_collection> </test> </tests> <help><![CDATA[ Select one or several zip archives with MTF (Multiple TSV Files) sets, stationary/instationary labeling type and possibly some advanced option to run the tool. Detailed documentation is available on https://influx-si.readthedocs.io ]]></help> <citations> <citation type="bibtex"> @misc{githubinflux, author = {Sokol, Serguei}, year = {2023}, title = {influx_s}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/sgsokol/influx}, } </citation> <citation type="doi">10.1093/bioinformatics/btr716</citation> </citations> </tool>