Mercurial > repos > tduigou > doe_synbio_sampler
changeset 4:d69cb64336e7 draft default tip
planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 537d7fefe58984b8f7ca66010153a2fdc35ddf4b
| author | tduigou |
|---|---|
| date | Wed, 14 Feb 2024 15:24:19 +0000 |
| parents | 0111a6eb7b98 |
| children | |
| files | sampler.xml test-data/converter_proCFPS_parameters.tsv test-data/sampler/input/parameters.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, 215 insertions(+), 224 deletions(-) [+] |
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--- a/sampler.xml Mon Jul 03 10:38:35 2023 +0000 +++ b/sampler.xml Wed Feb 14 15:24:19 2024 +0000 @@ -2,7 +2,7 @@ <description>Generate data points using latin hypercube sampling (LHS)</description> <macros> <import>macros.xml</import> - <token name="@TOOL_VERSION@">2.1.1</token> + <token name="@TOOL_VERSION@">2.2.0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">icfree</requirement> @@ -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[
--- a/test-data/converter_proCFPS_parameters.tsv Mon Jul 03 10:38:35 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/parameters.tsv Wed Feb 14 15:24:19 2024 +0000 @@ -0,0 +1,9 @@ +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
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