annotate 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

<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="[e-mail]" 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 &#x27;1,2&#x27; 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 =&gt; 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&#x27;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 &#x27;mc[=N]&#x27;, 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 &lt;= netflux &lt;= 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 &gt;= 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: &#x27;&#x27; (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: &#x27;1:10&#x27; -- use only first ten starting points; &#x27;1,3&#x27; -- use the the first and third starting points; &#x27;1:10,15,91:100&#x27; -- a mix of both formats is allowed. Default: &#x27;&#x27; (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&lt;identifier_0&gt;[^/]+)_res/(?P&lt;identifier_1&gt;[^/]+)\.(?P&lt;ext&gt;[^.]+)" 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>