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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 20770dfcb79499aa201b8b6faed420babef8d053
author tduigou
date Tue, 23 Jul 2024 09:30:33 +0000
parents 596e600be71f
children
files sampler.xml test-data/converter_proCFPS_parameters.tsv test-data/sampler/input/components.tsv test-data/sampler/output/sampling.test-1.tsv test-data/sampler/output/sampling.test-2.tsv test-data/sampler_sampling.test-1.tsv test-data/sampler_sampling.test-2.tsv
diffstat 7 files changed, 33 insertions(+), 299 deletions(-) [+]
line wrap: on
line diff
--- a/sampler.xml	Mon Jul 03 10:38:21 2023 +0000
+++ b/sampler.xml	Tue Jul 23 09:30:33 2024 +0000
@@ -1,37 +1,28 @@
 <tool id="doe_synbio_sampler" name="iCFree sampler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
-    <description>Generate data points using latin hypercube sampling (LHS)</description>
+    <description>Generate Latin Hypercube Samples for given components.</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@TOOL_VERSION@">2.1.1</token>
+        <token name="@TOOL_VERSION@">2.4.0</token>
     </macros>
     <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">icfree</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">icfree-ml</requirement>
     </requirements>
     <expand macro="stdio"/>
     <command detect_errors="exit_code"><![CDATA[
         python -m icfree.sampler
-            '$cfps_file'
-            --nb-sampling-steps '$adv.nb_sampling_steps'
-            --nb-samples '$nb_samples'
-            #if str($adv.sampling_ratio) != ""
-                #set ratios = ' '.join(['"' + $x + '"' for $x in $adv.sampling_ratio.split()])
-                --sampling-ratios $ratios
-            #end if
+            '$input_file'
+            '$output_sampling'
+            '$num_samples'
+            --step '$adv.step'
             #if str($adv.seed_cond.seed_param) == 'not_random'
                 --seed '$adv.seed_cond.seed'
             #end if
-            --output-format 'tsv'
-            --output-folder . &&
-            mv sampling.tsv '$output_sampling'
     ]]></command>
     <inputs>
-        <param name="cfps_file" type="data" format="tabular" label="CFPS parameters and features" />
-        <param name="nb_samples" type="integer" value="99" min="1" max="198" label="Number of samples to generate" />
+        <param name="input_file" type="data" format="tabular" label="Input file with components and their max values." />
+        <param name="num_samples" type="integer" value="99" min="1" max="198" label="Number of samples to generate" />
         <section name="adv" title="Advanced Options" expanded="false">
-            <param name="nb_sampling_steps" type="integer" value="5" min="1" max="10" label="Number of values for all factors when performing the sampling" />
-            <param name="sampling_ratio" type="text" value="" label="Ratios associated for all factors" help="Only float, space separated, are allowed">
-                <validator type="regex" message="Float separated by a space between in the range: 0.0 - 1.0">^(?:(0.\d+|1\.0)(\s0?\.\d+|1\.0)*)*$</validator>
-            </param>
+            <param name="step" type="float" value="2.5" min="1" max="10" label="Step size for creating discrete ranges" />
             <conditional name="seed_cond">
                 <param name="seed_param" type="select" label="Seed" help="Choose a seed or let it as random">
                     <option value="random" selected="true">random</option>
@@ -53,80 +44,27 @@
     <tests>
         <!-- test 1: check if identical outputs are produced with default parameters  -->
         <test>
-            <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
+            <param name="input_file" value="sampler/input/components.tsv" />
+            <param name="num_samples" value="3" />
             <param name="seed_param" value="not_random" />
             <param name="seed" value="0" />
-            <output name="output_sampling" file="sampler_sampling.test-1.tsv" ftype="tabular" compare="diff" />
+            <output name="output_sampling" file="sampler/output/sampling.test-1.tsv" ftype="tabular" compare="diff" />
         </test>
-        <!-- test 2: advanced arguments -->
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
         <test>
-            <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
-            <param name="nb_sampling_steps" value="3" />
-            <param name="nb_samples" value="100" />
-            <param name="sampling_ratio" value="0.4 0.2 0.3" />
+            <param name="input_file" value="sampler/input/components.tsv" />
+            <param name="num_samples" value="4" />
+            <param name="step" value="3.1" />
             <param name="seed_param" value="not_random" />
             <param name="seed" value="0" />
-            <param name="nb_samples" value="100" />
-            <output name="output_sampling" file="sampler_sampling.test-2.tsv" ftype="tabular" compare="diff" />
+            <output name="output_sampling" file="sampler/output/sampling.test-2.tsv" ftype="tabular" compare="diff" />
         </test>
     </tests>
     <help><![CDATA[
 Sampler
 =======
 
-This module generates a list of values for all parameters given in the input file.
-The values are generated using a Latin Hypercube Sampling (LHS) method (lhs function from the pyDOE package).
-The number of values generated is given by the user and the values are saved in csv or tsv file.
-
-It is important to note that the user can pass some values that he whishes to combine. In this case, we are dealing with discrete space, and because LHS is working on continuous space the result sampling can contain duplicates.
-To avoid this, we have set some filters to select the appropriate sampling method:
-
-* If the result sampling contain duplicates, then we replace them by random samples.
-* Proceed with full random sampling.
-* Generate all the combinations.
-
-Input
------
-
-Below is an example of an input file:
-
-+-----------+----------+---------------------+
-| Parameter | maxValue | Ratios              |
-+===========+==========+=====================+
-| CP        | 125      | 0.0 0.1 0.3 0.5 1.0 |
-+-----------+----------+---------------------+
-| CPK       | 125      | 1                   |
-+-----------+----------+---------------------+
-| tRNA      | 125      |                     |
-+-----------+----------+---------------------+
-| AA        | 125      |                     |
-+-----------+----------+---------------------+
-| ribosomes | 125      |                     |
-+-----------+----------+---------------------+
-| mRNA      | 125      |                     |
-+-----------+----------+---------------------+
-| Mg        | 125      |                     |
-+-----------+----------+---------------------+
-| K         | 125      |                     |
-+-----------+----------+---------------------+
-
-The first column is the parameter (or factor) names.
-
-The second column is the maxValue of the parameter that will be used in the sampling.
-
-The third column is the specific ratios we want to have for this parameter. If nothing defined, then take ratios given in program options.
-If one single number is given, then take this number as a const value.
-If no value is given, then take the default ratios (`nb_samples` linear ratios from 0 to 1).
-
-Advanced options:
------------------
-* **Number of sampling steps**: Number of values for all factors when performing the sampling (default: 5)
-* **Sampling ratios**: Ratios for all factors when performing the sampling
-* **Number of samples**: Number of samples to generate for all factors when performing the sampling (default: 99)
-
-Output
-------
-* a TSV file with the sampling values for each parameter
+Generate Latin Hypercube Samples for given components.
     ]]></help>
     <expand macro="creator"/>
     <citations>
--- a/test-data/converter_proCFPS_parameters.tsv	Mon Jul 03 10:38:21 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-Parameter	maxValue	stockConcentration	deadVolume	Ratios
-Mg-glutamate	4	168	0	0.0 0.1 0.3 0.5 1.0
-k-glutamate	80	3360	0	
-CoA	0.26	210	0	
-3-PGA	30	1400	0	
-NTP	1.5	630	0	
-NAD	0.33	138.6	0	
-Folinic acid	0.068	28.56	0	
-Spermidine	1	420	0	
-tRNA	0.2	84	0	
-Amino acids	1.5	6	0	
-CAMP	0.75	200	0	
-Extract	30	300	2000	1
-HEPES	50	2100	0	1
-PEG	2	200	4000	1
-Promoter	10	300	0	1
-RBS	10	200	0	1
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampler/input/components.tsv	Tue Jul 23 09:30:33 2024 +0000
@@ -0,0 +1,5 @@
+Component	maxValue
+Hela lysate	1000
+Access prot 50%	400
+Reaction mix	400
+RNA 1ug/uL	200
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampler/output/sampling.test-1.tsv	Tue Jul 23 09:30:33 2024 +0000
@@ -0,0 +1,4 @@
+Hela lysate,Access prot 50%,Reaction mix,RNA 1ug/uL
+492.5,25.0,310.0,152.5
+970.0,165.0,257.5,112.5
+537.5,325.0,192.5,185.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampler/output/sampling.test-2.tsv	Tue Jul 23 09:30:33 2024 +0000
@@ -0,0 +1,5 @@
+Hela lysate,Access prot 50%,Reaction mix,RNA 1ug/uL
+610.7,403.0,378.2,52.7
+666.5,384.40000000000003,282.1,111.60000000000001
+62.0,319.3,170.5,52.7
+409.2,238.70000000000002,399.90000000000003,37.2
--- a/test-data/sampler_sampling.test-1.tsv	Mon Jul 03 10:38:21 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-Mg-glutamate	k-glutamate	CoA	3-PGA	NTP	NAD	Folinic acid	Spermidine	tRNA	Amino acids	CAMP	Extract	HEPES	PEG	Promoter	RBS
-2.0	20.0	0.26	0.0	1.5	0.2475	0.0	0.25	0.05	0.375	0.75	30.0	50.0	2.0	10.0	10.0
-2.0	80.0	0.26	7.5	1.5	0.0	0.068	0.5	0.05	1.5	0.5625	30.0	50.0	2.0	10.0	10.0
-2.0	20.0	0.0	15.0	1.125	0.0	0.017	0.25	0.0	1.125	0.1875	30.0	50.0	2.0	10.0	10.0
-2.0	20.0	0.26	22.5	0.0	0.165	0.051000000000000004	0.0	0.05	0.375	0.75	30.0	50.0	2.0	10.0	10.0
-1.2	0.0	0.0	15.0	1.5	0.33	0.017	0.25	0.2	1.5	0.75	30.0	50.0	2.0	10.0	10.0
-1.2	20.0	0.195	0.0	0.0	0.165	0.051000000000000004	0.5	0.05	0.375	0.75	30.0	50.0	2.0	10.0	10.0
-0.4	80.0	0.0	0.0	0.375	0.2475	0.0	0.0	0.05	1.125	0.75	30.0	50.0	2.0	10.0	10.0
-0.0	20.0	0.195	30.0	1.125	0.0825	0.034	1.0	0.2	1.5	0.1875	30.0	50.0	2.0	10.0	10.0
-2.0	20.0	0.13	7.5	1.5	0.33	0.0	0.25	0.15000000000000002	0.375	0.1875	30.0	50.0	2.0	10.0	10.0
-2.0	40.0	0.065	0.0	0.0	0.165	0.051000000000000004	0.5	0.1	0.0	0.0	30.0	50.0	2.0	10.0	10.0
-2.0	80.0	0.195	7.5	1.125	0.0825	0.068	0.25	0.05	1.5	0.75	30.0	50.0	2.0	10.0	10.0
-0.4	40.0	0.195	7.5	0.75	0.0825	0.051000000000000004	1.0	0.15000000000000002	0.0	0.375	30.0	50.0	2.0	10.0	10.0
-4.0	60.0	0.13	22.5	1.125	0.33	0.068	0.75	0.15000000000000002	1.125	0.0	30.0	50.0	2.0	10.0	10.0
-0.4	80.0	0.13	7.5	0.75	0.0825	0.034	0.0	0.1	0.0	0.0	30.0	50.0	2.0	10.0	10.0
-4.0	60.0	0.0	7.5	1.5	0.0	0.034	0.25	0.05	1.125	0.5625	30.0	50.0	2.0	10.0	10.0
-4.0	80.0	0.065	7.5	1.5	0.2475	0.0	1.0	0.0	0.375	0.5625	30.0	50.0	2.0	10.0	10.0
-2.0	0.0	0.26	22.5	0.375	0.0	0.051000000000000004	0.5	0.0	1.5	0.5625	30.0	50.0	2.0	10.0	10.0
-0.0	60.0	0.0	22.5	1.5	0.33	0.017	0.5	0.05	0.75	0.0	30.0	50.0	2.0	10.0	10.0
-0.4	60.0	0.065	30.0	1.125	0.2475	0.0	0.5	0.15000000000000002	0.0	0.1875	30.0	50.0	2.0	10.0	10.0
-1.2	0.0	0.26	15.0	0.375	0.33	0.068	1.0	0.05	0.375	0.5625	30.0	50.0	2.0	10.0	10.0
-1.2	60.0	0.26	22.5	0.375	0.0	0.068	1.0	0.1	1.125	0.5625	30.0	50.0	2.0	10.0	10.0
-0.0	40.0	0.065	7.5	0.375	0.0	0.0	0.75	0.15000000000000002	0.375	0.1875	30.0	50.0	2.0	10.0	10.0
-1.2	20.0	0.13	0.0	0.0	0.0825	0.034	1.0	0.2	1.125	0.75	30.0	50.0	2.0	10.0	10.0
-4.0	20.0	0.195	7.5	1.125	0.2475	0.068	0.5	0.0	1.125	0.375	30.0	50.0	2.0	10.0	10.0
-1.2	40.0	0.195	30.0	1.125	0.0825	0.034	0.75	0.15000000000000002	0.375	0.0	30.0	50.0	2.0	10.0	10.0
-1.2	40.0	0.195	30.0	0.0	0.0	0.0	1.0	0.0	0.0	0.375	30.0	50.0	2.0	10.0	10.0
-0.0	0.0	0.065	0.0	0.75	0.0	0.034	0.75	0.0	0.75	0.375	30.0	50.0	2.0	10.0	10.0
-0.4	20.0	0.0	30.0	1.125	0.165	0.034	0.0	0.05	1.125	0.0	30.0	50.0	2.0	10.0	10.0
-0.4	0.0	0.195	0.0	0.75	0.2475	0.0	0.5	0.1	1.5	0.75	30.0	50.0	2.0	10.0	10.0
-2.0	0.0	0.0	22.5	0.375	0.165	0.068	0.5	0.05	0.75	0.5625	30.0	50.0	2.0	10.0	10.0
-4.0	60.0	0.195	7.5	1.125	0.33	0.068	0.0	0.2	1.5	0.75	30.0	50.0	2.0	10.0	10.0
-0.0	0.0	0.065	30.0	1.125	0.33	0.017	0.0	0.0	0.375	0.1875	30.0	50.0	2.0	10.0	10.0
-2.0	60.0	0.065	15.0	0.0	0.165	0.068	0.75	0.2	0.75	0.1875	30.0	50.0	2.0	10.0	10.0
-1.2	20.0	0.0	22.5	0.375	0.0	0.068	0.5	0.1	0.75	0.0	30.0	50.0	2.0	10.0	10.0
-0.4	40.0	0.13	7.5	0.75	0.0	0.017	1.0	0.0	0.375	0.375	30.0	50.0	2.0	10.0	10.0
-1.2	20.0	0.065	15.0	1.5	0.0	0.017	0.75	0.2	1.125	0.1875	30.0	50.0	2.0	10.0	10.0
-0.0	0.0	0.0	0.0	1.125	0.165	0.034	0.75	0.0	0.75	0.5625	30.0	50.0	2.0	10.0	10.0
-4.0	80.0	0.13	7.5	0.375	0.2475	0.034	0.75	0.1	0.0	0.75	30.0	50.0	2.0	10.0	10.0
-4.0	80.0	0.065	0.0	0.375	0.33	0.034	0.25	0.0	0.0	0.1875	30.0	50.0	2.0	10.0	10.0
-1.2	0.0	0.13	30.0	0.75	0.0	0.0	0.25	0.2	0.0	0.75	30.0	50.0	2.0	10.0	10.0
-0.4	40.0	0.13	15.0	0.375	0.33	0.0	0.25	0.1	0.0	0.0	30.0	50.0	2.0	10.0	10.0
-4.0	80.0	0.195	0.0	0.75	0.0	0.0	0.0	0.15000000000000002	0.0	0.375	30.0	50.0	2.0	10.0	10.0
-2.0	20.0	0.26	30.0	0.375	0.165	0.068	0.25	0.2	0.375	0.375	30.0	50.0	2.0	10.0	10.0
-0.4	80.0	0.26	22.5	0.75	0.0825	0.068	1.0	0.2	1.5	0.0	30.0	50.0	2.0	10.0	10.0
-1.2	60.0	0.26	7.5	1.5	0.33	0.068	1.0	0.15000000000000002	0.75	0.1875	30.0	50.0	2.0	10.0	10.0
-4.0	80.0	0.0	22.5	0.75	0.0	0.034	0.25	0.0	1.5	0.1875	30.0	50.0	2.0	10.0	10.0
-4.0	80.0	0.195	22.5	0.0	0.33	0.051000000000000004	0.75	0.15000000000000002	0.375	0.0	30.0	50.0	2.0	10.0	10.0
-1.2	60.0	0.13	15.0	1.125	0.33	0.0	0.0	0.05	1.125	0.375	30.0	50.0	2.0	10.0	10.0
-2.0	0.0	0.0	22.5	0.375	0.2475	0.051000000000000004	0.75	0.05	0.75	0.1875	30.0	50.0	2.0	10.0	10.0
-0.4	0.0	0.195	7.5	0.75	0.165	0.051000000000000004	0.5	0.0	1.125	0.1875	30.0	50.0	2.0	10.0	10.0
-0.4	0.0	0.065	7.5	0.375	0.2475	0.051000000000000004	0.5	0.1	0.375	0.0	30.0	50.0	2.0	10.0	10.0
-0.4	80.0	0.195	15.0	0.375	0.33	0.0	0.25	0.2	0.0	0.75	30.0	50.0	2.0	10.0	10.0
-0.4	60.0	0.13	7.5	0.0	0.0825	0.0	0.75	0.05	1.5	0.5625	30.0	50.0	2.0	10.0	10.0
-1.2	40.0	0.26	22.5	1.5	0.0	0.0	0.25	0.05	0.75	0.0	30.0	50.0	2.0	10.0	10.0
-0.0	0.0	0.26	15.0	0.0	0.165	0.051000000000000004	0.5	0.2	0.0	0.375	30.0	50.0	2.0	10.0	10.0
-2.0	60.0	0.26	0.0	0.0	0.0825	0.034	0.75	0.15000000000000002	0.0	0.0	30.0	50.0	2.0	10.0	10.0
-1.2	40.0	0.065	30.0	0.0	0.2475	0.068	0.75	0.15000000000000002	0.75	0.5625	30.0	50.0	2.0	10.0	10.0
-0.0	60.0	0.13	0.0	0.75	0.2475	0.034	0.75	0.15000000000000002	0.375	0.375	30.0	50.0	2.0	10.0	10.0
-4.0	0.0	0.195	15.0	1.125	0.165	0.017	0.25	0.2	1.125	0.75	30.0	50.0	2.0	10.0	10.0
-4.0	40.0	0.13	7.5	1.5	0.33	0.051000000000000004	0.0	0.15000000000000002	1.125	0.375	30.0	50.0	2.0	10.0	10.0
-0.4	40.0	0.0	30.0	1.125	0.0825	0.017	1.0	0.2	0.375	0.1875	30.0	50.0	2.0	10.0	10.0
-2.0	80.0	0.13	30.0	1.125	0.33	0.068	0.0	0.2	0.75	0.75	30.0	50.0	2.0	10.0	10.0
-4.0	80.0	0.065	30.0	1.5	0.0825	0.017	0.75	0.2	1.5	0.75	30.0	50.0	2.0	10.0	10.0
-1.2	20.0	0.195	0.0	0.0	0.165	0.034	0.75	0.15000000000000002	0.75	0.5625	30.0	50.0	2.0	10.0	10.0
-2.0	40.0	0.065	22.5	1.125	0.0825	0.051000000000000004	1.0	0.0	1.125	0.0	30.0	50.0	2.0	10.0	10.0
-0.0	80.0	0.195	7.5	1.5	0.0825	0.034	1.0	0.0	1.5	0.375	30.0	50.0	2.0	10.0	10.0
-2.0	60.0	0.13	30.0	0.0	0.165	0.017	0.25	0.0	0.0	0.375	30.0	50.0	2.0	10.0	10.0
-1.2	0.0	0.26	30.0	1.125	0.33	0.051000000000000004	0.0	0.1	1.125	0.75	30.0	50.0	2.0	10.0	10.0
-0.4	20.0	0.0	30.0	1.5	0.2475	0.034	0.25	0.1	1.5	0.5625	30.0	50.0	2.0	10.0	10.0
-1.2	20.0	0.26	7.5	0.75	0.2475	0.034	0.0	0.05	1.5	0.0	30.0	50.0	2.0	10.0	10.0
-0.4	0.0	0.0	0.0	0.75	0.2475	0.017	1.0	0.1	1.5	0.5625	30.0	50.0	2.0	10.0	10.0
-4.0	60.0	0.0	7.5	0.375	0.0	0.051000000000000004	0.75	0.1	1.125	0.0	30.0	50.0	2.0	10.0	10.0
-4.0	0.0	0.195	22.5	0.0	0.165	0.068	1.0	0.0	0.375	0.75	30.0	50.0	2.0	10.0	10.0
-4.0	20.0	0.13	0.0	0.75	0.2475	0.051000000000000004	0.25	0.15000000000000002	0.75	0.375	30.0	50.0	2.0	10.0	10.0
-0.0	40.0	0.26	0.0	1.5	0.33	0.017	0.5	0.1	1.5	0.0	30.0	50.0	2.0	10.0	10.0
-0.0	20.0	0.0	30.0	0.375	0.0	0.017	0.0	0.0	1.5	0.0	30.0	50.0	2.0	10.0	10.0
-0.0	40.0	0.0	15.0	1.5	0.33	0.0	0.75	0.1	0.375	0.1875	30.0	50.0	2.0	10.0	10.0
-4.0	60.0	0.13	0.0	1.125	0.0825	0.051000000000000004	0.0	0.2	0.75	0.1875	30.0	50.0	2.0	10.0	10.0
-0.0	0.0	0.065	22.5	0.75	0.2475	0.017	1.0	0.05	0.75	0.5625	30.0	50.0	2.0	10.0	10.0
-2.0	0.0	0.065	15.0	0.0	0.165	0.068	0.0	0.05	1.5	0.1875	30.0	50.0	2.0	10.0	10.0
-2.0	60.0	0.13	15.0	0.75	0.0825	0.017	0.5	0.0	0.0	0.75	30.0	50.0	2.0	10.0	10.0
-0.0	60.0	0.0	30.0	0.0	0.0	0.051000000000000004	0.5	0.15000000000000002	1.125	0.75	30.0	50.0	2.0	10.0	10.0
-0.4	40.0	0.065	15.0	0.375	0.2475	0.051000000000000004	0.75	0.15000000000000002	0.75	0.5625	30.0	50.0	2.0	10.0	10.0
-0.0	40.0	0.26	22.5	0.375	0.0	0.0	0.75	0.05	1.125	0.0	30.0	50.0	2.0	10.0	10.0
-0.0	60.0	0.13	22.5	0.0	0.2475	0.034	0.25	0.05	0.0	0.1875	30.0	50.0	2.0	10.0	10.0
-0.0	80.0	0.26	30.0	0.75	0.0	0.0	0.0	0.2	0.75	0.375	30.0	50.0	2.0	10.0	10.0
-4.0	20.0	0.065	15.0	0.0	0.33	0.017	0.0	0.2	1.125	0.5625	30.0	50.0	2.0	10.0	10.0
-4.0	80.0	0.195	15.0	0.0	0.2475	0.017	0.5	0.15000000000000002	0.375	0.375	30.0	50.0	2.0	10.0	10.0
-2.0	80.0	0.195	0.0	0.375	0.0825	0.017	0.0	0.2	0.0	0.1875	30.0	50.0	2.0	10.0	10.0
-0.4	0.0	0.0	0.0	1.5	0.165	0.068	1.0	0.2	1.5	0.0	30.0	50.0	2.0	10.0	10.0
-0.0	60.0	0.26	22.5	0.75	0.33	0.0	0.25	0.0	0.75	0.75	30.0	50.0	2.0	10.0	10.0
-0.0	80.0	0.0	0.0	0.375	0.165	0.017	0.5	0.1	0.0	0.5625	30.0	50.0	2.0	10.0	10.0
-0.0	80.0	0.13	22.5	1.5	0.165	0.068	0.25	0.1	0.0	0.5625	30.0	50.0	2.0	10.0	10.0
-0.4	60.0	0.065	30.0	1.125	0.2475	0.068	1.0	0.15000000000000002	0.75	0.1875	30.0	50.0	2.0	10.0	10.0
-4.0	40.0	0.26	15.0	1.125	0.0825	0.034	0.0	0.1	0.0	0.375	30.0	50.0	2.0	10.0	10.0
-1.2	20.0	0.065	22.5	1.5	0.165	0.051000000000000004	0.5	0.0	1.5	0.375	30.0	50.0	2.0	10.0	10.0
-0.4	40.0	0.26	15.0	0.0	0.0825	0.051000000000000004	1.0	0.15000000000000002	0.375	0.375	30.0	50.0	2.0	10.0	10.0
-1.2	40.0	0.195	30.0	1.5	0.0825	0.017	1.0	0.1	1.125	0.5625	30.0	50.0	2.0	10.0	10.0
-2.0	20.0	0.065	15.0	0.75	0.0825	0.0	0.0	0.1	0.375	0.5625	30.0	50.0	2.0	10.0	10.0
--- a/test-data/sampler_sampling.test-2.tsv	Mon Jul 03 10:38:21 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,101 +0,0 @@
-Mg-glutamate	k-glutamate	CoA	3-PGA	NTP	NAD	Folinic acid	Spermidine	tRNA	Amino acids	CAMP	Extract	HEPES	PEG	Promoter	RBS
-2.0	32.0	0.052000000000000005	9.0	0.44999999999999996	0.066	0.013600000000000001	0.2	0.06	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.078	6.0	0.30000000000000004	0.099	0.013600000000000001	0.4	0.04000000000000001	0.6000000000000001	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.4	24.0	0.052000000000000005	12.0	0.6000000000000001	0.099	0.013600000000000001	0.4	0.06	0.30000000000000004	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.4	16.0	0.10400000000000001	6.0	0.30000000000000004	0.066	0.027200000000000002	0.2	0.08000000000000002	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-4.0	16.0	0.052000000000000005	6.0	0.44999999999999996	0.099	0.0204	0.3	0.04000000000000001	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.4	16.0	0.052000000000000005	12.0	0.30000000000000004	0.099	0.013600000000000001	0.4	0.06	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.4	24.0	0.078	6.0	0.30000000000000004	0.066	0.013600000000000001	0.4	0.06	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.078	12.0	0.30000000000000004	0.066	0.0204	0.3	0.08000000000000002	0.44999999999999996	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-1.2	32.0	0.10400000000000001	9.0	0.30000000000000004	0.066	0.013600000000000001	0.2	0.04000000000000001	0.44999999999999996	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.4	16.0	0.052000000000000005	12.0	0.6000000000000001	0.132	0.0204	0.2	0.04000000000000001	0.30000000000000004	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-4.0	24.0	0.052000000000000005	9.0	0.44999999999999996	0.132	0.0204	0.4	0.08000000000000002	0.30000000000000004	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-1.2	16.0	0.078	6.0	0.30000000000000004	0.132	0.0204	0.4	0.04000000000000001	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-4.0	24.0	0.078	9.0	0.44999999999999996	0.099	0.0204	0.4	0.08000000000000002	0.44999999999999996	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-4.0	24.0	0.10400000000000001	6.0	0.6000000000000001	0.066	0.013600000000000001	0.3	0.08000000000000002	0.44999999999999996	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.4	32.0	0.078	12.0	0.6000000000000001	0.099	0.027200000000000002	0.4	0.04000000000000001	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-1.2	32.0	0.078	6.0	0.6000000000000001	0.099	0.027200000000000002	0.4	0.08000000000000002	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-2.0	24.0	0.078	9.0	0.6000000000000001	0.066	0.013600000000000001	0.3	0.06	0.30000000000000004	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-4.0	32.0	0.10400000000000001	12.0	0.6000000000000001	0.066	0.0204	0.2	0.06	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-1.2	32.0	0.078	9.0	0.6000000000000001	0.099	0.0204	0.2	0.04000000000000001	0.44999999999999996	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.052000000000000005	6.0	0.44999999999999996	0.099	0.0204	0.3	0.04000000000000001	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-1.2	16.0	0.052000000000000005	9.0	0.6000000000000001	0.099	0.0204	0.2	0.08000000000000002	0.30000000000000004	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-2.0	24.0	0.052000000000000005	12.0	0.6000000000000001	0.099	0.027200000000000002	0.4	0.06	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.4	32.0	0.10400000000000001	6.0	0.44999999999999996	0.066	0.013600000000000001	0.2	0.06	0.30000000000000004	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-2.0	32.0	0.052000000000000005	12.0	0.6000000000000001	0.099	0.027200000000000002	0.4	0.06	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.0	16.0	0.10400000000000001	12.0	0.30000000000000004	0.066	0.0204	0.4	0.06	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.4	24.0	0.052000000000000005	6.0	0.6000000000000001	0.132	0.013600000000000001	0.4	0.06	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.052000000000000005	6.0	0.44999999999999996	0.132	0.013600000000000001	0.3	0.08000000000000002	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.4	32.0	0.052000000000000005	6.0	0.44999999999999996	0.132	0.013600000000000001	0.3	0.08000000000000002	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.4	16.0	0.078	9.0	0.44999999999999996	0.132	0.0204	0.2	0.08000000000000002	0.44999999999999996	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.0	32.0	0.078	6.0	0.6000000000000001	0.099	0.013600000000000001	0.2	0.04000000000000001	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-1.2	32.0	0.10400000000000001	12.0	0.44999999999999996	0.066	0.0204	0.4	0.06	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-4.0	32.0	0.10400000000000001	12.0	0.30000000000000004	0.132	0.013600000000000001	0.2	0.08000000000000002	0.44999999999999996	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-2.0	24.0	0.052000000000000005	9.0	0.44999999999999996	0.132	0.027200000000000002	0.4	0.04000000000000001	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-2.0	32.0	0.052000000000000005	9.0	0.44999999999999996	0.132	0.013600000000000001	0.2	0.08000000000000002	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-4.0	32.0	0.052000000000000005	6.0	0.44999999999999996	0.066	0.0204	0.2	0.08000000000000002	0.44999999999999996	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-1.2	16.0	0.052000000000000005	12.0	0.30000000000000004	0.099	0.0204	0.2	0.06	0.30000000000000004	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-2.0	24.0	0.078	12.0	0.6000000000000001	0.099	0.027200000000000002	0.2	0.08000000000000002	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-1.2	16.0	0.078	6.0	0.6000000000000001	0.099	0.0204	0.4	0.04000000000000001	0.6000000000000001	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-2.0	24.0	0.052000000000000005	12.0	0.6000000000000001	0.066	0.027200000000000002	0.3	0.06	0.6000000000000001	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.078	12.0	0.44999999999999996	0.132	0.027200000000000002	0.3	0.08000000000000002	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-1.2	24.0	0.10400000000000001	12.0	0.30000000000000004	0.132	0.027200000000000002	0.3	0.08000000000000002	0.6000000000000001	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-2.0	16.0	0.10400000000000001	12.0	0.30000000000000004	0.066	0.013600000000000001	0.4	0.08000000000000002	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-2.0	24.0	0.10400000000000001	9.0	0.30000000000000004	0.132	0.027200000000000002	0.4	0.04000000000000001	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-2.0	16.0	0.10400000000000001	9.0	0.30000000000000004	0.066	0.0204	0.2	0.06	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.078	6.0	0.44999999999999996	0.066	0.0204	0.2	0.04000000000000001	0.6000000000000001	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-2.0	16.0	0.078	6.0	0.30000000000000004	0.066	0.013600000000000001	0.3	0.04000000000000001	0.6000000000000001	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-2.0	16.0	0.078	12.0	0.44999999999999996	0.066	0.013600000000000001	0.3	0.06	0.30000000000000004	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-1.2	16.0	0.052000000000000005	12.0	0.6000000000000001	0.099	0.027200000000000002	0.4	0.08000000000000002	0.6000000000000001	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-2.0	32.0	0.078	12.0	0.6000000000000001	0.066	0.027200000000000002	0.4	0.04000000000000001	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-4.0	16.0	0.052000000000000005	6.0	0.44999999999999996	0.132	0.027200000000000002	0.3	0.06	0.30000000000000004	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-1.2	32.0	0.052000000000000005	6.0	0.30000000000000004	0.132	0.013600000000000001	0.4	0.06	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.0	32.0	0.052000000000000005	6.0	0.44999999999999996	0.066	0.027200000000000002	0.2	0.04000000000000001	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-4.0	24.0	0.052000000000000005	6.0	0.44999999999999996	0.066	0.0204	0.3	0.04000000000000001	0.44999999999999996	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-2.0	32.0	0.078	9.0	0.6000000000000001	0.066	0.013600000000000001	0.4	0.04000000000000001	0.30000000000000004	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-4.0	32.0	0.052000000000000005	6.0	0.30000000000000004	0.099	0.0204	0.2	0.06	0.44999999999999996	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.4	24.0	0.078	9.0	0.30000000000000004	0.132	0.013600000000000001	0.2	0.04000000000000001	0.44999999999999996	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-2.0	24.0	0.052000000000000005	9.0	0.44999999999999996	0.132	0.013600000000000001	0.3	0.08000000000000002	0.44999999999999996	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-2.0	16.0	0.078	9.0	0.6000000000000001	0.066	0.013600000000000001	0.3	0.06	0.30000000000000004	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.4	16.0	0.078	6.0	0.30000000000000004	0.132	0.027200000000000002	0.3	0.08000000000000002	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.10400000000000001	6.0	0.6000000000000001	0.132	0.027200000000000002	0.3	0.08000000000000002	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-4.0	32.0	0.10400000000000001	9.0	0.6000000000000001	0.066	0.0204	0.3	0.04000000000000001	0.44999999999999996	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-1.2	24.0	0.10400000000000001	6.0	0.6000000000000001	0.099	0.027200000000000002	0.2	0.08000000000000002	0.44999999999999996	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.0	16.0	0.10400000000000001	9.0	0.6000000000000001	0.066	0.027200000000000002	0.4	0.06	0.30000000000000004	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-4.0	32.0	0.10400000000000001	6.0	0.6000000000000001	0.099	0.013600000000000001	0.3	0.06	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.4	32.0	0.078	9.0	0.44999999999999996	0.066	0.013600000000000001	0.2	0.04000000000000001	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-1.2	16.0	0.10400000000000001	9.0	0.30000000000000004	0.132	0.013600000000000001	0.4	0.04000000000000001	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.10400000000000001	6.0	0.6000000000000001	0.066	0.0204	0.4	0.04000000000000001	0.30000000000000004	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-4.0	16.0	0.052000000000000005	6.0	0.44999999999999996	0.099	0.013600000000000001	0.4	0.06	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.4	24.0	0.10400000000000001	9.0	0.44999999999999996	0.132	0.0204	0.3	0.08000000000000002	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-4.0	32.0	0.052000000000000005	9.0	0.6000000000000001	0.132	0.013600000000000001	0.3	0.06	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-4.0	24.0	0.10400000000000001	9.0	0.44999999999999996	0.132	0.027200000000000002	0.2	0.08000000000000002	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.4	16.0	0.078	12.0	0.6000000000000001	0.099	0.013600000000000001	0.4	0.04000000000000001	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.4	16.0	0.052000000000000005	9.0	0.30000000000000004	0.066	0.027200000000000002	0.2	0.08000000000000002	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-1.2	16.0	0.078	9.0	0.30000000000000004	0.099	0.0204	0.2	0.06	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.4	32.0	0.10400000000000001	9.0	0.6000000000000001	0.132	0.027200000000000002	0.2	0.06	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-1.2	24.0	0.10400000000000001	12.0	0.30000000000000004	0.132	0.0204	0.3	0.06	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-1.2	32.0	0.10400000000000001	12.0	0.30000000000000004	0.132	0.0204	0.2	0.04000000000000001	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.078	12.0	0.30000000000000004	0.099	0.013600000000000001	0.3	0.04000000000000001	0.30000000000000004	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.0	16.0	0.078	6.0	0.6000000000000001	0.099	0.013600000000000001	0.4	0.06	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.052000000000000005	12.0	0.30000000000000004	0.099	0.0204	0.3	0.04000000000000001	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.0	16.0	0.078	9.0	0.6000000000000001	0.099	0.0204	0.4	0.04000000000000001	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-4.0	32.0	0.078	12.0	0.30000000000000004	0.132	0.027200000000000002	0.3	0.06	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-4.0	24.0	0.078	9.0	0.30000000000000004	0.066	0.027200000000000002	0.4	0.06	0.30000000000000004	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-1.2	16.0	0.10400000000000001	6.0	0.44999999999999996	0.132	0.0204	0.4	0.08000000000000002	0.30000000000000004	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-4.0	24.0	0.10400000000000001	12.0	0.30000000000000004	0.132	0.027200000000000002	0.2	0.06	0.6000000000000001	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-0.0	32.0	0.052000000000000005	12.0	0.30000000000000004	0.066	0.0204	0.3	0.04000000000000001	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-2.0	16.0	0.078	6.0	0.44999999999999996	0.132	0.013600000000000001	0.4	0.08000000000000002	0.44999999999999996	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-4.0	16.0	0.10400000000000001	12.0	0.44999999999999996	0.066	0.027200000000000002	0.3	0.08000000000000002	0.6000000000000001	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-1.2	16.0	0.052000000000000005	6.0	0.30000000000000004	0.132	0.013600000000000001	0.2	0.04000000000000001	0.44999999999999996	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.4	16.0	0.10400000000000001	9.0	0.44999999999999996	0.099	0.027200000000000002	0.2	0.04000000000000001	0.30000000000000004	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-2.0	16.0	0.10400000000000001	12.0	0.30000000000000004	0.132	0.027200000000000002	0.2	0.08000000000000002	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-4.0	32.0	0.052000000000000005	12.0	0.44999999999999996	0.066	0.0204	0.4	0.08000000000000002	0.6000000000000001	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-1.2	32.0	0.052000000000000005	9.0	0.44999999999999996	0.099	0.027200000000000002	0.3	0.08000000000000002	0.44999999999999996	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.4	32.0	0.078	6.0	0.44999999999999996	0.132	0.0204	0.3	0.06	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-1.2	32.0	0.052000000000000005	9.0	0.30000000000000004	0.099	0.027200000000000002	0.3	0.08000000000000002	0.44999999999999996	0.30000000000000004	30.0	50.0	2.0	10.0	10.0
-2.0	32.0	0.078	9.0	0.44999999999999996	0.099	0.027200000000000002	0.3	0.04000000000000001	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.4	32.0	0.10400000000000001	12.0	0.30000000000000004	0.066	0.0204	0.2	0.06	0.30000000000000004	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.0	24.0	0.10400000000000001	6.0	0.6000000000000001	0.099	0.013600000000000001	0.2	0.04000000000000001	0.30000000000000004	0.22499999999999998	30.0	50.0	2.0	10.0	10.0
-0.0	16.0	0.10400000000000001	9.0	0.44999999999999996	0.066	0.027200000000000002	0.2	0.08000000000000002	0.30000000000000004	0.15000000000000002	30.0	50.0	2.0	10.0	10.0
-0.0	16.0	0.10400000000000001	12.0	0.6000000000000001	0.099	0.027200000000000002	0.3	0.04000000000000001	0.6000000000000001	0.15000000000000002	30.0	50.0	2.0	10.0	10.0