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Updating doe_synbio from version 2.1.2 to 2.2.0 #169

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merged 4 commits into from
Feb 14, 2024
Merged

Updating doe_synbio from version 2.1.2 to 2.2.0 #169

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c95df13
Updating doe_synbio from version 2.1.2 to 2.1.3
guillaume-gricourt Dec 18, 2023
146c874
Updating doe_synbio from version 2.1.3 to 2.2.0
guillaume-gricourt Dec 25, 2023
96b80a2
fix(tools): doe_synbio, update test
guillaume-gricourt Feb 14, 2024
873378c
fix(tools): doe_synbio, rm urls
guillaume-gricourt Feb 14, 2024
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34 changes: 17 additions & 17 deletions tools/doe_synbio/optdoe.xml
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Expand Up @@ -187,23 +187,23 @@ Above are examples of two constructs generated through optimal combinatorial des
Note: if advanced parameter "input_parts" is left empty, the following parts are used:


+---------+------------+--------------------------------------------------+
| Name | Type | SynBioHub |
+=========+============+==================================================+
| PlacUV5 | Promoter | https://synbiohub.org/public/igem/BBa_K1847014/1 |
+---------+------------+--------------------------------------------------+
| Ptrc | Promoter | https://synbiohub.org/public/igem/BBa_J56012/1 |
+---------+------------+--------------------------------------------------+
| BBR1 | Origin | https://synbiohub.org/public/igem/BBa_I50041/1 |
+---------+------------+--------------------------------------------------+
| p15A | Origin | https://synbiohub.org/public/igem/BBa_I50032/1 |
+---------+------------+--------------------------------------------------+
| ColE1 | Origin | https://synbiohub.org/public/igem/BBa_J64101/1 |
+---------+------------+--------------------------------------------------+
| res1 | Resistance | https://synbiohub.org/public/igem/BBa_I13800/1 |
+---------+------------+--------------------------------------------------+
| Ter | Terminator | https://synbiohub.org/public/igem/BBa_B1006/1 |
+---------+------------+--------------------------------------------------+
+---------+------------+--------------+
| Name | Type | SynBioHub |
+=========+============+==============+
| PlacUV5 | Promoter | BBa_K1847014 |
+---------+------------+--------------+
| Ptrc | Promoter | BBa_J56012 |
+---------+------------+--------------+
| BBR1 | Origin | BBa_I50041 |
+---------+------------+--------------+
| p15A | Origin | BBa_I50032 |
+---------+------------+--------------+
| ColE1 | Origin | BBa_J64101 |
+---------+------------+--------------+
| res1 | Resistance | BBa_I13800 |
+---------+------------+--------------+
| Ter | Terminator | BBa_B1006 |
+---------+------------+--------------+

The source of this file can be found here as a model: https://raw.githubusercontent.com/pablocarb/doebase/master/doebase/data/ref_parts.csv

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11 changes: 5 additions & 6 deletions tools/doe_synbio/sampler.xml
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Expand Up @@ -2,7 +2,7 @@
<description>Generate data points using latin hypercube sampling (LHS)</description>
<macros>
<import>macros.xml</import>
<token name="@TOOL_VERSION@">2.1.2</token>
<token name="@TOOL_VERSION@">2.2.0</token>
</macros>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">icfree</requirement>
Expand Down Expand Up @@ -53,21 +53,20 @@
<tests>
<!-- test 1: check if identical outputs are produced with default parameters -->
<test>
<param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
<param name="cfps_file" value="sampler/input/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" />
<output name="output_sampling" file="sampler/output/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="cfps_file" value="sampler/input/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" />
<output name="output_sampling" file="sampler/output/sampling.test-2.tsv" ftype="tabular" compare="diff" />
</test>
</tests>
<help><![CDATA[
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17 changes: 0 additions & 17 deletions tools/doe_synbio/test-data/converter_proCFPS_parameters.tsv
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9 changes: 9 additions & 0 deletions tools/doe_synbio/test-data/sampler/input/parameters.tsv
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Component maxValue Ratios
Component_1 125 0.0 0.1 0.3 0.5 1.0
Component_2 125 1
Component_3 125
Component_4 125
Component_5 125
Component_6 125
Component_7 125
Component_8 125
100 changes: 100 additions & 0 deletions tools/doe_synbio/test-data/sampler/output/sampling.test-1.tsv
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101 changes: 101 additions & 0 deletions tools/doe_synbio/test-data/sampler/output/sampling.test-2.tsv
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