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changeset 0:164616ec7f18 draft

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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
author tduigou
date Tue, 28 Mar 2023 12:32:38 +0000
parents
children 81b079d1642c
files config/tool_conf.xml img/image3.png img/image46.png macros.xml sampler.xml test-data/converter_proCFPS_parameters.tsv test-data/genes_lycopene.csv test-data/sampler_sampling.test-1.tsv test-data/sampler_sampling.test-2.tsv
diffstat 9 files changed, 357 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/tool_conf.xml	Tue Mar 28 12:32:38 2023 +0000
@@ -0,0 +1,3 @@
+  <section id="sbc-gd" name="SynBioCAD Genetic Design">
+    <tool file="synbiocad-galaxy-wrappers/optdoe/optdoe.xml" />
+  </section>
Binary file img/image3.png has changed
Binary file img/image46.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Mar 28 12:32:38 2023 +0000
@@ -0,0 +1,15 @@
+<macros>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@LICENSE@">MIT</token>
+    <xml name="stdio">
+        <stdio>
+            <regex match="WARNING" level="warning" />
+            <regex match="ERROR" level="fatal" />
+        </stdio>
+    </xml>
+    <xml name="creator">
+        <creator>
+            <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
+        </creator>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sampler.xml	Tue Mar 28 12:32:38 2023 +0000
@@ -0,0 +1,112 @@
+<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>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@TOOL_VERSION@">2.1.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">icfree</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 $ratios
+            #end if
+            #if str($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" />
+        <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)*)*$</validator>
+            </param>
+            <conditional name="seed_cond">
+                <param name="seed_param" type="select" label="Seed" help="Choose a seed or let it as random">
+                    <option value="random" selected="true">random</option>
+                    <option value="not_random">fixed</option>
+                </param>
+                <when value="random"/>
+                <when value="not_random">
+                    <param name="seed" type="text" value="0" label="Seed value" help="Only integer allowed">
+                        <validator type="empty_field" message="Not empty, select random"/>
+                        <validator type="regex" message="Only integer allowed">^(?:\d+)$</validator>
+                    </param>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_sampling" format="tabular" label="${tool.name}" />
+    </outputs>
+    <tests>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+        <test>
+            <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
+            <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" />
+        </test>
+        <!-- test 2: advanced arguments -->
+        <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="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" />
+        </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
+-----
+* **CFPS Parameters File**: 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 concnetration of the stock. The fourth column is the deadVolume of the parameter. This is used to calculate the volume of the parameter that will not be pipetted by the robot (because of viscosity). The fifth 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.
+
+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
+    ]]></help>
+    <expand macro="creator"/>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{icfree
+                author = {Joan Hérisson, Yorgo El Moubayed},
+                title = {{icfree}},
+                url = {https://github.com/brsynth/icfree-ml/},
+            }
+        </citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/converter_proCFPS_parameters.tsv	Tue Mar 28 12:32:38 2023 +0000
@@ -0,0 +1,17 @@
+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/genes_lycopene.csv	Tue Mar 28 12:32:38 2023 +0000
@@ -0,0 +1,9 @@
+Name,Type,Part,Step
+P21684,gene,P21684,1
+P21683,gene,P21683,1
+P21683,gene,P21683,2
+P21684,gene,P21684,2
+P21685,gene,P21685,3
+P21683,gene,P21683,3
+P21687,gene,P21687,3
+P21688,gene,P21688,3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampler_sampling.test-1.tsv	Tue Mar 28 12:32:38 2023 +0000
@@ -0,0 +1,100 @@
+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
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+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
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+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
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+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampler_sampling.test-2.tsv	Tue Mar 28 12:32:38 2023 +0000
@@ -0,0 +1,101 @@
+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