# HG changeset patch
# User tduigou
# Date 1680006772 0
# Node ID cae2975d264fee31bfdd747c8be2591141026a79
planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 6c01728900e4ebd1a833a7e7d697f61561d86dc6-dirty
diff -r 000000000000 -r cae2975d264f config/tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/config/tool_conf.xml Tue Mar 28 12:32:52 2023 +0000
@@ -0,0 +1,3 @@
+
diff -r 000000000000 -r cae2975d264f img/image3.png
Binary file img/image3.png has changed
diff -r 000000000000 -r cae2975d264f img/image46.png
Binary file img/image46.png has changed
diff -r 000000000000 -r cae2975d264f macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Mar 28 12:32:52 2023 +0000
@@ -0,0 +1,15 @@
+
+ 0
+ MIT
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diff -r 000000000000 -r cae2975d264f optdoe.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/optdoe.xml Tue Mar 28 12:32:52 2023 +0000
@@ -0,0 +1,241 @@
+
+ Combine selected genetic parts and enzyme variants for the desired pathways
+
+ macros.xml
+ v2.0.2
+
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+ doebase
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+ `_ for more codons.
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+Output
+------
+
+* **Constructs**\ : Output SBOL file. It contains some combinations of constructs according to the algorithm described above.
+ ]]>
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+ @unpublished{pablocarb
+ author = {Pablo Carbonell},
+ title = {{doebase}},
+ url = {https://github.com/pablocarb/doebase/},
+ }
+
+
+
diff -r 000000000000 -r cae2975d264f test-data/converter_proCFPS_parameters.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/converter_proCFPS_parameters.tsv Tue Mar 28 12:32:52 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
diff -r 000000000000 -r cae2975d264f test-data/genes_lycopene.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes_lycopene.csv Tue Mar 28 12:32:52 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
diff -r 000000000000 -r cae2975d264f test-data/sampler_sampling.test-1.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampler_sampling.test-1.tsv Tue Mar 28 12:32:52 2023 +0000
@@ -0,0 +1,100 @@
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diff -r 000000000000 -r cae2975d264f test-data/sampler_sampling.test-2.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampler_sampling.test-2.tsv Tue Mar 28 12:32:52 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
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