annotate influx_si.xml @ 1:4e3d4318113b draft

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit e9183269ad5b2e8f4551f301dc736df330aa73c6

<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 &#x27;1,2&#x27; 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 &#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="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 &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="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 &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="--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&#x27;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: &#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="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>