influx_si v7.0.1_1

tools/influx_si/README.rst

@@ -2,19 +2,22 @@
 Metabolic flux estimation
 -------------------------
 
-`influx_si` can be used for metabolic flux estimation based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). Tha name `influx_si` is used as common for both tools.
+`influx_si` can be used for estimation of metabolic fluxes and concentrations   based on labeling data from MS and/or NMR measurements. `influx_s` is used for stationary labeling and `influx_i` for instationary one (hence the '_s' and '_i' in the names). The name `influx_si` is used as common for both tools.
 
-The input for `influx_si` in one or several FTBL files, each describing a given labeling experiment and options to use during estimation. In addition, for `influx_i` a file with time course data has to be provided for each FTBL file.
+The input for `influx_si` is an MTF (Multiple TSV Files) collection describing metabolic network, label transition, labeling data and options to use during estimation.
 
-The output is a zip archive with files generated by `influx_si`. Among the most important is file ending with `_res.kvh` which contains the main information about estimated parameters, their statistics and so on.
-If, in your FTBL file, you have requested ploting information, it can be found in respective .pdf file.
+The output is a zip archive with files generated by `influx_si`. File ending with `.tvar.sim` which contains the estimated fluxes and concentrations. Other files ending with `.sim` contain simulated measurements. File ending with `.stat` has results of chi2 test assessing quality of fit.
 
-For detailed documentation about `influx_si` and accompanying tools see https://metasys.insa-toulouse.fr/software/influx/doc/
+If, in your `.opt` file, you have requested plotting information (`plot_smeas.R` or `plot_ilab.R`), it can be found in the respective `.pdf` file.
 
-For getting a standalone version of `influx_si` see https://metasys.insa-toulouse.fr/software/influx/
+For detailed documentation about `influx_si` and accompanying tools see https://influx-si.readthedocs.io
+
+For getting a standalone version of `influx_si <https://anaconda.org/bioconda/influx_si>`_, you can install it e.g. with `conda <https://docs.conda.io/en/latest/miniconda.html>`_ package manager: ::
+
+ conda install -c conda-forge -c bioconda influx_si
 
 Author: Serguei Sokol
 
 License: GPL2
 
-© INRAE 2020
+© INRAE/INSA/CNRS 2023

tools/influx_si/macros.xml

@@ -0,0 +1,154 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">7.0.1</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@COMMAND_OPT@"><![CDATA[
+    $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
+]]>
+    </token>
+    <token name="@MTF_OPT@"><![CDATA[
+        #if $opt.mtf:
+            --mtf '$opt.mtf'
+        #end if
+]]>
+    </token>
+    <xml name="inputs">
+        <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>
+    </xml>
+    <xml name="help">
+        <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>
+    </xml>
+    <xml name="citation">
+        <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>
+    </xml>
+</macros>