Repository 'optdoe'
hg clone https://toolshed.g2.bx.psu.edu/repos/tduigou/optdoe

Changeset 3:34e11d0590fa (2023-05-01)
Previous changeset 2:593e0f787172 (2022-10-24)
Commit message:
planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
added:
config/job_conf.xml
config/tool_conf.xml
img/image3.png
img/image46.png
macros.xml
test-data/converter_proCFPS_parameters.tsv
test-data/sampler_sampling.test-1.tsv
test-data/sampler_sampling.test-2.tsv
removed:
optdoe.xml
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diff -r 593e0f787172 -r 34e11d0590fa config/job_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/config/job_conf.xml Mon May 01 01:29:51 2023 +0000
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+    <tool id="optdoe" destination="local" />
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diff -r 593e0f787172 -r 34e11d0590fa config/tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/config/tool_conf.xml Mon May 01 01:29:51 2023 +0000
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+  <section id="sbc-gd" name="SynBioCAD Genetic Design">
+    <tool file="synbiocad-galaxy-wrappers/optdoe/optdoe.xml" />
+  </section>
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diff -r 593e0f787172 -r 34e11d0590fa img/image3.png
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Binary file img/image3.png has changed
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diff -r 593e0f787172 -r 34e11d0590fa img/image46.png
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Binary file img/image46.png has changed
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diff -r 593e0f787172 -r 34e11d0590fa macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon May 01 01:29:51 2023 +0000
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+<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>
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diff -r 593e0f787172 -r 34e11d0590fa optdoe.xml
--- a/optdoe.xml Mon Oct 24 10:22:28 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,262 +0,0 @@\n-<tool id="optdoe" name="Design of Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">\n-    <description>An optimal design of experiments (DoE) base package for synthetic biology</description>\n-    <macros>\n-        <token name="@VERSION_SUFFIX@">0</token>\n-        <token name="@TOOL_VERSION@">2.0.2</token>\n-    </macros>\n-    <requirements>\n-        <requirement type="package" version="@TOOL_VERSION@">doebase</requirement>\n-    </requirements>\n-    <command detect_errors="exit_code"><![CDATA[\n-        python -m doebase\n-            --func doeGetSBOL\n-            #if $adv.genes_sbol_file\n-                --sbol_file \'$adv.genes_sbol_file\'\n-            #end if\n-            #if $adv.ref_parts_file\n-                --ref_parts_file \'$adv.ref_parts_file\'\n-            #end if\n-            --libsize \'$adv.libsize\'\n-            $adv.get_sequences\n-            $adv.backtranslate\n-            --codon_table \'$adv.codon_table\'\n-            \'$genes_file\'\n-            \'$constructs\'\n-    ]]></command>\n-    <inputs>\n-        <param name="genes_file" type="data" format="csv" label="Genes" help="CSV file with header: Name,Type,Part,Step. Provided by the tool Selenzyme"/>\n-        <section name="adv" title="Advanced Options" expanded="false">\n-            <param name="genes_sbol_file" type="data" format="xml" optional="true" label="Optimised Genes" help="SBOL file with genes associated with different RBS. Provided by the tool PartsGenie"/>\n-            <param argument="--ref_parts_file" type="data" format="csv" value="None" optional="true" label="Ref Parts (default: E. coli compliant)" help="Provide fixed parts"/>\n-            <param argument="--libsize" type="integer" value="32" min="32" label="Maximal library size" help="Maximal number of contructs in the output"/>\n-            <param argument="--get_sequences" type="boolean" truevalue="--get_sequences true" falsevalue="--get_sequences false" checked="true" label="Get sequences" help="Grab the sequence for each part of the SBOL output"/>\n-            <param argument="--backtranslate" type="boolean" truevalue="--backtranslate true" falsevalue="--backtranslate false" checked="true" label="Back translate" help="Translate the protein sequence given by its Uniprot ID to a DNA sequence"/>\n-            <param argument="--codon_table" type="select" label="Codon Table">\n-                <option value="Eecoli.cut">Escherichia coli K12</option>\n-                <option value="Ehuman.cut">Homo sapiens</option>\n-                <option value="Eacica.cut">Acinetobacter calcoaceticus</option>\n-                <option value="Eagrtu.cut">Agrobacterium tumefaciens str C58</option>\n-                <option value="Eanasp.cut">Anabaena sp</option>\n-                <option value="Earath.cut">Arabidopsis thaliana</option>\n-                <option value="Eazovi.cut">Azotobacter vinelandii</option>\n-                <option value="Ebacme.cut">Bacillus megaterium</option>\n-                <option value="Ebacst.cut">Geobacillus stearothermophilus</option>\n-                <option value="Ebacsu.cut">Bacillus subtilis</option>\n-                <option value="Ebacsu_high.cut">Bacillus subtilis (high)</option>\n-                <option value="Ebommo.cut">Bombyx mori (silkmoth)</option>\n-                <option value="Ebovin.cut">Bos taurus</option>\n-                <option value="Ebpphx.cut">Bacteriophage phi-X174</option>\n-                <option value="Ebraja.cut">Bradyrhizobium japonicum USDA 110</option>\n-                <option value="Ebrana.cut">Brassica napus (rape)</option>\n-                <option value="Ebrare.cut">Brachydanio rerio (zebrafish)</option>\n-                <option value="Ecaeel.cut">Caenorhabditis elegans (nematode)</option>\n-                <option value="Ecanal.cut">Candida albicans</option>\n-                <option value="Ecanfa.cut">Canis familiaris (dog)</option>\n-                <option value="Ecaucr.cut">Caulobacter crescentus CB15</option>\n-         '..b'ttps://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/OptDoE/img/image3.png\n-\t:width: 80 %\n-\t:align: center\n-\n-\n-.. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/OptDoE/img/image46.png\n-\t:width: 80 %\n-\t:align: center\n-\n-|\n-\n-Above are examples of two constructs generated through optimal combinatorial design and represented using SBOL Visual in SynBioHub.\n-Note: if advanced parameter "input_parts" is left empty, the following parts are used:\n-\n-\n-    +---------+------------+--------------------------------------------------+\n-    | Name    | Type       | SynBioHub                                        |\n-    +=========+============+==================================================+\n-    | PlacUV5 | Promoter   | https://synbiohub.org/public/igem/BBa_K1847014/1 |\n-    +---------+------------+--------------------------------------------------+\n-    | Ptrc    | Promoter   | https://synbiohub.org/public/igem/BBa_J56012/1   |\n-    +---------+------------+--------------------------------------------------+\n-    | BBR1    | Origin     | https://synbiohub.org/public/igem/BBa_I50041/1   |\n-    +---------+------------+--------------------------------------------------+\n-    | p15A    | Origin     | https://synbiohub.org/public/igem/BBa_I50032/1   |\n-    +---------+------------+--------------------------------------------------+\n-    | ColE1   | Origin     | https://synbiohub.org/public/igem/BBa_J64101/1   |\n-    +---------+------------+--------------------------------------------------+\n-    | res1    | Resistance | https://synbiohub.org/public/igem/BBa_I13800/1   |\n-    +---------+------------+--------------------------------------------------+\n-    | Ter     | Terminator | https://synbiohub.org/public/igem/BBa_B1006/1    |\n-    +---------+------------+--------------------------------------------------+\n-\t  \n-The source of this file can be found here as a model: https://raw.githubusercontent.com/pablocarb/doebase/master/doebase/data/ref_parts.csv\n-\n-Input\n------\n-\n-Required:\n-\n-* **Genes**\\ : Output of Selenzyme. The CSV file contains four columnds: Name,Type,Part,Step. The column "Name" contains the Uniprot ID found by Selenzyme. The column "Type" represents the type of the "Part", a *gene*. The column "Part" has the same information as the column "Name". The column "Step" contains the order of the position in the pathway of the gene.\n-\n-Advanced options:\n-\n-* **Optimised Genes**\\ : SBOL file containing optimized versions of the genes associated with different RBS. Output of the PartsGenie tool.\n-* **Ref Parts**\\ : CSV with the genetic parts. Default (if left empty) is the above table. To generate a new compatible CSV file, please use the "OptDoE Parts Reference Generator" tool\n-* **Maximal library size**\\ : (integer, default: 32) Maximal number of constructs in the SBOL output. \n-* **Get sequences**\\ : (boolean, default: True) Grab the sequence for each part of the SBOL output.\n-* **Back translate**\\ : (boolean, default: True) Translate the protein sequence given by its Uniprot ID to a DNA sequence.\n-* **Codon Table**\\ : (text, default: Eecoli.cut) Codon Usage Table. See `codon_table <https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBOSS+backtranseq+Help+and+Documentation#EMBOSSbacktranseqHelpandDocumentation-WebServices>`_ for more codons.\n-\n-Output\n-------\n-\n-* **Constructs**\\ : Output SBOL file. It contains some combinations of constructs according to the algorithm described above.\n-\n-Project Link\n-------------\n-\n-* `Original Project <https://github.com/pablocarb/doebase>`_\n-\n-License\n--------\n-\n-`MIT <https://raw.githubusercontent.com/pablocarb/appoptdes/master/LICENSE>`_\n-\n-Acknowledgments\n----------------\n-\n-* Joan H\xc3\xa9risson\n-* Thomas Duigou\n-    ]]></help>\n-    <creator>\n-        <person givenName="Pablo" familyName="Carbonell" email="pablo.carbonell@upv.es" identifier="https://orcid.org/0000-0002-0993-5625" />\n-    </creator>\n-</tool>\n\\ No newline at end of file\n'
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diff -r 593e0f787172 -r 34e11d0590fa test-data/converter_proCFPS_parameters.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/converter_proCFPS_parameters.tsv Mon May 01 01:29:51 2023 +0000
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+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
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diff -r 593e0f787172 -r 34e11d0590fa 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 Mon May 01 01:29:51 2023 +0000
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b
diff -r 593e0f787172 -r 34e11d0590fa 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 Mon May 01 01:29:51 2023 +0000
b
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