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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit e9183269ad5b2e8f4551f301dc736df330aa73c6
| author | workflow4metabolomics |
|---|---|
| date | Wed, 13 Sep 2023 19:52:44 +0000 |
| parents | 9b03a930b08b |
| children | 57f199aa07e4 |
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<tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy1"> <description>metabolic flux analysis</description> <macros> <token name="@TOOL_VERSION@">5.1.0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">influx_si</requirement> </requirements> <version_command>influx_s --version</version_command> <command detect_errors="exit_code"><![CDATA[ #set $inp_all = [$input_main, ($prlexp.input_aux if $prlexp.input_aux else [])] #if $si.s_i == 'i': #silent $inp_all.append($si.input_ti) #end if mkdir outdir && cd outdir && #for $inp in $inp_all: #for $i in $inp: ln -s '$i' '$i.element_identifier' && #end for #end for influx_$si.s_i $opt.noopt $opt.noscale #if $opt.meth != 'None': $opt.meth #end if $opt.fullsys $opt.emu $opt.irand #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 $opt.ln $opt.sln $opt.tikhreg $opt.lim #if $opt.zc: --zc='$opt.zc' #end if $opt.ffguess #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 $opt.nocalc $opt.addnoise $opt.TIMEIT #if $opt.tblimit: --tblimit='$opt.tblimit' #end if #if $si.s_i == 'i' and $si.time_order: --time_order='$si.time_order' #end if '${"' '".join([str($in_m.element_identifier) for $in_m in $input_main])}' > 'influx_${si.s_i}.stdout.txt' 2>'influx_${si.s_i}.stderr.txt'; res="\$?" && for f in *.ftbl *.log *.err *.R *.kvh *.attrs; do mv -f "\$f" "\$f".txt || true; done && for f in *.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done && for f in *.RData; do [ -e "\$f" ] && mv -f "\$f" "\$f".RData || true; done && [ "\$res" == "0" ] ]]></command> <inputs> <param type="data" name="input_main" format="ftbl" multiple="true" label="main FTBL(s): network+data"/> <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 type="data" name="input_ti" label="time course data" format="txt,tsv" multiple="true"/> <param argument="--time_order" type="select" label="time order for ODE solving" optional="true" help="Order 2 is more precise but more time consuming. The value '1,2' makes to start solving the ODE with the first order scheme then continues with the order 2."> <option value="None">None</option> <option value="1">1</option> <option value="2">2</option> <option value="1,2">1,2</option> </param> </when> </conditional> <section name="prlexp" title="Parallel labeling experiments" expanded="false"> <param optional="true" type="data" name="input_aux" format="ftbl" multiple="True" label="auxiliary FTBL(s): data only"/> </section> <section name="opt" title="Advanced Options" expanded="false"> <param argument="--noopt" type="boolean" checked="false" truevalue="--noopt" falsevalue="" label="no optimization" optional="true" help=", 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="no scaling factors to optimize" optional="true" help="all scaling factors are assumed to be 1" /> <param argument="--meth" type="select" label="method for optimization" optional="true"> <option value="--meth=BFGS">BFGS</option> <option value="--meth=Nelder-Mead">Nelder-Mead</option> <option value="--meth=nlsic">nlsic</option> </param> <param argument="--fullsys" type="boolean" checked="false" truevalue="--fullsys" falsevalue="" label="full cumomer system" optional="true" help="calculate all cumomer set (not just the reduced one necesary to simulate measurements)" /> <param argument="--emu" type="boolean" checked="false" truevalue="--emu" falsevalue="" label="simulate labeling in EMU approach" optional="true" /> <param argument="--irand" type="boolean" checked="false" truevalue="--irand" falsevalue="" label="random initial approximation" optional="true" help="ignore initial approximation for free parameters (free fluxes and metabolite concentrations) from the FTBL file (cf. also --iseries option) and use random values drawn uniformly from [0,1] interval" /> <param argument="--sens" type="text" value="" label="sensitivity method" optional="true" help="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="upper limit for reverse fluxes" optional="true" help="Must be in interval [0, 1]. Default: 0.999" /> <param argument="--cupn" type="float" min="0" value="" label="absolute limit for net fluxes" optional="true" help="-cupn <= netflux <= cupn. Must be non negative. Value 0 means no limit. Default: 1.e3" /> <param argument="--cupp" type="float" min="0" value="" label="upper limit for metabolite pool" optional="true" help="Default: 1.e5" /> <param argument="--clownr" type="float" min="0" value="" label="lower limit for not reversible free and dependent fluxes" optional="true" help="Zero value (default) means no lower limit" /> <param argument="--cinout" type="float" min="0" value="" label="lower limit for input/output free and dependent fluxes" optional="true" help="Must be non negative. Default: 0" /> <param argument="--clowp" type="float" min="0" value="" label="lower limit for free metabolite pools" optional="true" help="Must be positive. Default 1.e-8" /> <param argument="--np" type="float" min="0" value="" label="process number" 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="--ln" type="boolean" checked="false" truevalue="--ln" falsevalue="" label="least norm" optional="true" 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="solution least norm" optional="true" 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="use Tikhonov regularization" optional="true" 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="least norm from limSolve package" optional="true" help="The same as --ln but with a function limSolve::lsei()" /> <param argument="--zc" type="float" min="0" value="" label="zero crossing" optional="true" help="Apply zero crossing strategy with non negative threshold for net fluxes" /> <param argument="--ffguess" type="boolean" checked="false" truevalue="--ffguess" falsevalue="" label="free fluxes guess" optional="true" help="Don't use free/dependent flux definitions from FTBL file(s). Make an automatic guess." /> <param argument="--iseries" type="text" value="" label="indexes of starting points" optional="true" help="When used jointly with --irand, allows generating multiple random starting points. 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="random 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="threshold for excluding 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="--nocalc" type="boolean" checked="false" truevalue="--nocalc" falsevalue="" label="no calculation" optional="true" help="generate an R code but not execute it." /> <param argument="--addnoise" type="boolean" checked="false" truevalue="--addnoise" falsevalue="" label="add noise" optional="true" 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="measure timings" optional="true" help="developer option: measure cpu time or not" /> <param argument="--tblimit" type="integer" min="0" value="0" label="Python traceback limit" optional="true" help="developer option: set trace back limit for Python error messages" /> </section> </inputs> <outputs> <!-- TODO: this should probably not be a collection, also name_and_ext probably does not work correctly for all elements--> <collection name="influx_si_output" type="list" label="influx_${si.s_i}_on_${on_string}"> <discover_datasets pattern="__name_and_ext__" directory="outdir" visible="false"/> </collection> </outputs> <tests> <test> <param name="input_main" value="e_coli.ftbl" /> <conditional name="si"> <param name="s_i" value="s" /> </conditional> <output_collection name="influx_si_output" type="list" count="11"> <element name="e_coli.log" ftype="txt"> <assert_contents> <has_n_lines n="38"/> <has_line_matching expression="^end.*"/> </assert_contents> </element> </output_collection> </test> <test> <param name="input_main" value="e_coli.ftbl,e_coli_growth.ftbl" /> <conditional name="si"> <param name="s_i" value="s" /> </conditional> <output_collection name="influx_si_output" type="list"> <element name="e_coli_growth.log" ftype="txt"> <assert_contents> <has_n_lines n="45"/> <has_line_matching expression="^end.*"/> </assert_contents> </element> </output_collection> </test> <test> <param name="input_main" value="e_coli_i.ftbl" /> <conditional name="si"> <param name="s_i" value="i" /> <param name="input_ti" value="e_coli_msen.txt" /> <!--param name="time_order" value="1,2" /--> <!--How to pass single value with comma in it?--> </conditional> <output_collection name="influx_si_output" type="list"> <element name="e_coli_i.log" ftype="txt"> <assert_contents> <has_n_lines n="47"/> <has_line_matching expression="^end.*"/> </assert_contents> </element> </output_collection> </test> <test> <param name="input_main" value="e_coli_1-Glc_exact.ftbl" /> <param name="input_aux" value="e_coli_U-Glc_exact.ftbl" /> <conditional name="si"> <param name="s_i" value="s" /> </conditional> <output_collection name="influx_si_output" type="list"> <element name="e_coli_1-Glc_exact.log" ftype="txt"> <assert_contents> <has_n_lines n="40"/> <has_line_matching expression="^end.*"/> </assert_contents> </element> </output_collection> </test> </tests> <help><![CDATA[ Optimize free fluxes and optionaly metabolite concentrations of a given static metabolic network defined in an FTBL file to fit 13C data provided in the same FTBL file. ]]></help> <citations> <citation type="bibtex"> @misc{githubinflux, author = {Sokol, Serguei}, year = {2020}, 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>