Mercurial > repos > workflow4metabolomics > influx_si
diff 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 |
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--- a/influx_si.xml Wed Sep 13 19:52:44 2023 +0000 +++ b/influx_si.xml Wed Dec 13 08:56:04 2023 +0000 @@ -1,232 +1,204 @@ -<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 +<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 - $opt.fullsys - $opt.emu - $opt.irand #if $opt.sens: - --sens='$opt.sens' + --sens='$opt.sens' #end if #if $opt.cupx: - --cupx='$opt.cupx' + --cupx='$opt.cupx' #end if #if $opt.cupn: - --cupn='$opt.cupn' + --cupn='$opt.cupn' #end if #if $opt.cupp: - --cupp='$opt.cupp' + --cupp='$opt.cupp' #end if #if $opt.clownr: - --clownr='$opt.clownr' + --clownr='$opt.clownr' #end if #if $opt.cinout: - --cinout='$opt.cinout' + --cinout='$opt.cinout' #end if #if $opt.clowp: - --clowp='$opt.clowp' + --clowp='$opt.clowp' #end if #if $opt.np: - --np='$opt.np' + --np='$opt.np' + #end if + #if $opt.zc: + --zc='$opt.zc' #end if - $opt.ln - $opt.sln - $opt.tikhreg - $opt.lim - #if $opt.zc: - --zc='$opt.zc' + #if $opt.fseries: + --fseries='$opt.fseries' #end if - $opt.ffguess #if $opt.iseries: - --iseries='$opt.iseries' + --iseries='$opt.iseries' #end if #if $opt.seed: - --seed='$opt.seed' + --seed='$opt.seed' #end if #if $opt.excl_outliers: - --excl_outliers '$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 - $opt.nocalc - $opt.addnoise - $opt.TIMEIT - #if $opt.tblimit: - --tblimit='$opt.tblimit' + #for $inp in $input_main: + #set base = $inp.name[:-4] + --prefix "$base" + #end for + #if $opt.mtf: + --mtf '$opt.mtf' #end if + + || ret=\$?; - #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" ] + #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" 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> + <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>