Mercurial > repos > workflow4metabolomics > influx_si
annotate influx_si.xml @ 1:4e3d4318113b draft
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit e9183269ad5b2e8f4551f301dc736df330aa73c6
author | workflow4metabolomics |
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date | Wed, 13 Sep 2023 19:52:44 +0000 |
parents | 9b03a930b08b |
children | 57f199aa07e4 |
rev | line source |
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1
4e3d4318113b
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit e9183269ad5b2e8f4551f301dc736df330aa73c6
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1 <tool id="influx_si" name="influx_si" version="@TOOL_VERSION@+galaxy1"> |
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2 <description>metabolic flux analysis</description> |
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3 <macros> |
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4 <token name="@TOOL_VERSION@">5.1.0</token> |
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5 </macros> |
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6 <requirements> |
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7 <requirement type="package" version="@TOOL_VERSION@">influx_si</requirement> |
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8 </requirements> |
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9 <version_command>influx_s --version</version_command> |
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10 <command detect_errors="exit_code"><![CDATA[ |
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11 #set $inp_all = [$input_main, ($prlexp.input_aux if $prlexp.input_aux else [])] |
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12 #if $si.s_i == 'i': |
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13 #silent $inp_all.append($si.input_ti) |
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14 #end if |
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15 |
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16 mkdir outdir && cd outdir && |
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17 |
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18 #for $inp in $inp_all: |
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19 #for $i in $inp: |
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4e3d4318113b
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit e9183269ad5b2e8f4551f301dc736df330aa73c6
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20 ln -s '$i' '$i.element_identifier' && |
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21 #end for |
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22 #end for |
1
4e3d4318113b
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit e9183269ad5b2e8f4551f301dc736df330aa73c6
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23 |
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24 influx_$si.s_i |
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25 $opt.noopt |
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26 $opt.noscale |
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27 #if $opt.meth != 'None': |
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28 $opt.meth |
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29 #end if |
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30 $opt.fullsys |
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31 $opt.emu |
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32 $opt.irand |
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33 #if $opt.sens: |
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34 --sens='$opt.sens' |
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35 #end if |
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36 #if $opt.cupx: |
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37 --cupx='$opt.cupx' |
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38 #end if |
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39 #if $opt.cupn: |
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40 --cupn='$opt.cupn' |
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41 #end if |
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42 #if $opt.cupp: |
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43 --cupp='$opt.cupp' |
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44 #end if |
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45 #if $opt.clownr: |
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46 --clownr='$opt.clownr' |
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47 #end if |
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48 #if $opt.cinout: |
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49 --cinout='$opt.cinout' |
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50 #end if |
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51 #if $opt.clowp: |
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52 --clowp='$opt.clowp' |
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53 #end if |
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54 #if $opt.np: |
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55 --np='$opt.np' |
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56 #end if |
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57 $opt.ln |
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58 $opt.sln |
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59 $opt.tikhreg |
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60 $opt.lim |
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61 #if $opt.zc: |
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62 --zc='$opt.zc' |
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63 #end if |
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64 $opt.ffguess |
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65 #if $opt.iseries: |
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66 --iseries='$opt.iseries' |
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67 #end if |
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68 #if $opt.seed: |
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69 --seed='$opt.seed' |
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70 #end if |
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71 #if $opt.excl_outliers: |
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72 --excl_outliers '$opt.excl_outliers' |
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73 #end if |
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74 $opt.nocalc |
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75 $opt.addnoise |
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76 $opt.TIMEIT |
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77 #if $opt.tblimit: |
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78 --tblimit='$opt.tblimit' |
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79 #end if |
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80 |
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81 #if $si.s_i == 'i' and $si.time_order: |
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82 --time_order='$si.time_order' |
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83 #end if |
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4e3d4318113b
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/ commit e9183269ad5b2e8f4551f301dc736df330aa73c6
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84 '${"' '".join([str($in_m.element_identifier) for $in_m in $input_main])}' |
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85 > 'influx_${si.s_i}.stdout.txt' 2>'influx_${si.s_i}.stderr.txt'; res="\$?" && |
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86 |
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87 for f in *.ftbl *.log *.err *.R *.kvh *.attrs; do mv -f "\$f" "\$f".txt || true; done && |
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88 |
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89 for f in *.pdf; do [ -e "\$f" ] && mv -f "\$f" "\$f".pdf || true; done && |
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90 |
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91 for f in *.RData; do [ -e "\$f" ] && mv -f "\$f" "\$f".RData || true; done && |
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92 [ "\$res" == "0" ] |
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93 ]]></command> |
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94 <inputs> |
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95 <param type="data" name="input_main" format="ftbl" multiple="true" label="main FTBL(s): network+data"/> |
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96 <conditional name="si"> |
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97 <param name="s_i" type="select" label="labeling type" display="radio"> |
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98 <option value="s">stationary</option> |
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99 <option value="i">instationary</option> |
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100 </param> |
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101 <when value="s"/> |
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102 <when value="i"> |
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103 <param type="data" name="input_ti" label="time course data" format="txt,tsv" multiple="true"/> |
1
4e3d4318113b
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104 <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."> |
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105 <option value="None">None</option> |
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106 <option value="1">1</option> |
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107 <option value="2">2</option> |
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108 <option value="1,2">1,2</option> |
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109 </param> |
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110 </when> |
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111 </conditional> |
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112 <section name="prlexp" title="Parallel labeling experiments" expanded="false"> |
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113 <param optional="true" type="data" name="input_aux" format="ftbl" multiple="True" label="auxiliary FTBL(s): data only"/> |
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114 </section> |
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115 <section name="opt" title="Advanced Options" expanded="false"> |
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116 <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" /> |
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117 <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" /> |
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118 <param argument="--meth" type="select" label="method for optimization" optional="true"> |
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119 <option value="--meth=BFGS">BFGS</option> |
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120 <option value="--meth=Nelder-Mead">Nelder-Mead</option> |
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121 <option value="--meth=nlsic">nlsic</option> |
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122 </param> |
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123 <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)" /> |
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124 <param argument="--emu" type="boolean" checked="false" truevalue="--emu" falsevalue="" label="simulate labeling in EMU approach" optional="true" /> |
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125 <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" /> |
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126 <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" /> |
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127 <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" /> |
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128 <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" /> |
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129 <param argument="--cupp" type="float" min="0" value="" label="upper limit for metabolite pool" optional="true" help="Default: 1.e5" /> |
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130 <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" /> |
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131 <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" /> |
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132 <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" /> |
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133 <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." /> |
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134 <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" /> |
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135 <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" /> |
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136 <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" /> |
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137 <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()" /> |
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138 <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" /> |
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139 <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." /> |
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140 <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)" /> |
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141 <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." /> |
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142 <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." /> |
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143 <param argument="--nocalc" type="boolean" checked="false" truevalue="--nocalc" falsevalue="" label="no calculation" optional="true" help="generate an R code but not execute it." /> |
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144 <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" /> |
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145 <param argument="--TIMEIT" type="boolean" checked="false" truevalue="--TIMEIT" falsevalue="" label="measure timings" optional="true" help="developer option: measure cpu time or not" /> |
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146 <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" /> |
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147 </section> |
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148 </inputs> |
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149 <outputs> |
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150 <!-- TODO: this should probably not be a collection, also name_and_ext probably does not work correctly for all elements--> |
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151 <collection name="influx_si_output" type="list" label="influx_${si.s_i}_on_${on_string}"> |
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152 <discover_datasets pattern="__name_and_ext__" directory="outdir" visible="false"/> |
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153 </collection> |
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154 </outputs> |
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155 <tests> |
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156 <test> |
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157 <param name="input_main" value="e_coli.ftbl" /> |
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158 <conditional name="si"> |
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159 <param name="s_i" value="s" /> |
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160 </conditional> |
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161 <output_collection name="influx_si_output" type="list" count="11"> |
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162 <element name="e_coli.log" ftype="txt"> |
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163 <assert_contents> |
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164 <has_n_lines n="38"/> |
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165 <has_line_matching expression="^end.*"/> |
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166 </assert_contents> |
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167 </element> |
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168 </output_collection> |
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169 </test> |
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170 <test> |
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171 <param name="input_main" value="e_coli.ftbl,e_coli_growth.ftbl" /> |
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172 <conditional name="si"> |
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173 <param name="s_i" value="s" /> |
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174 </conditional> |
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175 <output_collection name="influx_si_output" type="list"> |
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176 <element name="e_coli_growth.log" ftype="txt"> |
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177 <assert_contents> |
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178 <has_n_lines n="45"/> |
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179 <has_line_matching expression="^end.*"/> |
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180 </assert_contents> |
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181 </element> |
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182 </output_collection> |
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183 </test> |
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184 <test> |
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185 <param name="input_main" value="e_coli_i.ftbl" /> |
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186 <conditional name="si"> |
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187 <param name="s_i" value="i" /> |
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188 <param name="input_ti" value="e_coli_msen.txt" /> |
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189 <!--param name="time_order" value="1,2" /--> <!--How to pass single value with comma in it?--> |
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190 </conditional> |
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191 <output_collection name="influx_si_output" type="list"> |
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192 <element name="e_coli_i.log" ftype="txt"> |
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193 <assert_contents> |
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194 <has_n_lines n="47"/> |
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195 <has_line_matching expression="^end.*"/> |
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196 </assert_contents> |
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197 </element> |
0
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198 </output_collection> |
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199 </test> |
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200 <test> |
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201 <param name="input_main" value="e_coli_1-Glc_exact.ftbl" /> |
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202 <param name="input_aux" value="e_coli_U-Glc_exact.ftbl" /> |
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203 <conditional name="si"> |
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204 <param name="s_i" value="s" /> |
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205 </conditional> |
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206 <output_collection name="influx_si_output" type="list"> |
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207 <element name="e_coli_1-Glc_exact.log" ftype="txt"> |
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208 <assert_contents> |
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209 <has_n_lines n="40"/> |
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210 <has_line_matching expression="^end.*"/> |
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211 </assert_contents> |
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212 </element> |
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213 </output_collection> |
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214 </test> |
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215 </tests> |
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216 <help><![CDATA[ |
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217 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. |
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218 ]]></help> |
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219 <citations> |
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220 <citation type="bibtex"> |
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221 @misc{githubinflux, |
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222 author = {Sokol, Serguei}, |
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223 year = {2020}, |
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224 title = {influx_s}, |
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225 publisher = {GitHub}, |
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226 journal = {GitHub repository}, |
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227 url = {https://github.com/sgsokol/influx}, |
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228 } |
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229 </citation> |
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230 <citation type="doi">10.1093/bioinformatics/btr716</citation> |
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231 </citations> |
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232 </tool> |