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Changeset 3:6dda0879d95a (2023-05-01)

Previous changeset 2:aeebb663a0d9 (2022-04-04) Next changeset 4:b450154dc448 (2023-05-30)

Commit message:
planemo upload for repository https://github.com/brsynth/DNA-BOT commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6

modified:
dnabot.xml

added:
config/job_conf.xml
config/tool_conf.xml
static/images/DNABOT_WF.PNG

removed:
test-data/dnabot_scripts.tar

diff -r aeebb663a0d9 -r 6dda0879d95a config/job_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/config/job_conf.xml Mon May 01 01:14:17 2023 +0000

@@ -0,0 +1,1 @@
+ <tool id="dnabot" destination="local" />

diff -r aeebb663a0d9 -r 6dda0879d95a config/tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/config/tool_conf.xml Mon May 01 01:14:17 2023 +0000

@@ -0,0 +1,3 @@
+  <section id="sbc-util" name="SynBioCAD Utilities">
+    <tool file="synbiocad-galaxy-wrappers/dnabot/dnabot.xml" />
+  </section>

diff -r aeebb663a0d9 -r 6dda0879d95a dnabot.xml
--- a/dnabot.xml Mon Apr 04 15:24:55 2022 +0000
+++ b/dnabot.xml Mon May 01 01:14:17 2023 +0000

[

@@ -21,7 +21,7 @@
         && tar -cvf '$dnabot_scripts' 'output'
     ]]></command>
     <inputs>
-        <param name="construct_file" type="data" format="csv" label="Source Construct" help="File listing constructs to be implemented."/>
+        <param name="construct_file" type="data" format="csv" label="Source Construct" help="CSV file listing constructs to be implemented where each row corresponds to one construct and consists of a sequence of BASIC linker and DNA part IDs (in an operon format)"/>
         <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" help="File(s) listing parts to be used in constructs." />
         <section name="adv" title="Advanced Options" expanded="false">
             <param name="default_settings_file" type="data" format="yaml" optional="true" label="Lab settings file" help="Yaml file providing labware IDs and parameter to be used in the Opentrons scripts." />
@@ -37,7 +37,7 @@
                 <option value="A10" >A10</option>
                 <option value="A11" selected="true">A11</option>
             </param>
-            <param argument="--soc_column" type="select" label="Column coordinate for SOC" help="Coordinate of the column plate providing SOC media for the transformation step.">
+            <param argument="--soc_column" type="select" label="Column coordinate for SOC" help="Coordinate of the column plate providing SOC (Super Optimal broth with Catabolite repression) media for the transformation step. SOC is a nutrient-rich culture media typically used for bacterial transformation.">
                 <option value="1" selected="true">1</option>
                 <option value="2" >2</option>
                 <option value="3" >3</option>
@@ -61,22 +61,36 @@
         
             <param name="construct_file" value="constructs.csv" />
             <param name="plate_files" value="user_parts_coords.csv,linker_parts_coords.csv"/>
-            <output name="dnabot_scripts" file="dnabot_scripts.tar" compare="sim_size" decompress="True"/>
+            <output name="dnabot_scripts" ftype="tar">
+                <assert_contents>
+                    <has_size value="153600" delta="10000"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
DNA-Bot
============

- **DNA-Bot** tool reads the list of constructs (previously produced by `rpBasicDesign <https://toolshed.g2.bx.psu.edu/view/iuc/rpbasicdesign/cdd6a526bdcf>`_) and the DNA-parts position on the source plates and generates a set of python scripts to drive an Opentrons liquid handling robot for building the plasmids using BASIC assembly method (as decribed in `Storch2015 <https://doi.org/10.1021/sb500356d>`_). Optional parameters can be set by the user to define the plastic labwares to be used, and set protocol parameters such as washing or incubation times for purification step by providing a YAML settings file.
+**DNA-Bot** tool reads the list of constructs where each row corresponds to one construct and consists of a sequence of BASIC (Biopart Assembly Standard for Idempotent Cloning) linker and DNA part IDs (in an operon format), and the DNA-parts position on the source plates. The tool generates a set of python scripts to drive an Opentrons liquid handling robot for building the plasmids using BASIC assembly method (as decribed in `Storch2015 <https://doi.org/10.1021/sb500356d>`_).
+
+These python scripts implement the **4 assembly steps**: clip reactions, purification, assembly and strain transformation. In short, the **Clip reactions** step prepares the mixes for the ligation of the individual DNA parts with the linkers; the **Purification** step purifies the linker-ligated DNA parts using magnetic beads and the Opentrons magnetic module; the **Assembly** step mixes the DNA purified parts to build the final constructs; while the **Transformation** step transforms the chassis micro-organism with the plasmid and inoculates onto agar.
+
+.. image:: ${static_path}/images/DNABOT_WF.PNG
+    :width: 90 %
+    :align: center
+
+|
+
+Optional parameters can be set by the user to define the plastic labwares to be used, and set protocol parameters such as washing or incubation times for purification step by providing a YAML settings file. Default settings: `<https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/dnabot/default_settings.yaml>`_

Inputs
------

-* **Source Construct**: CSV file listing constructs to be implemented.
+* **Source Construct**: CSV file listing constructs to be implemented where each row corresponds to one construct and consists of a sequence of BASIC linker and DNA part IDs (in an operon format).
* **Plate files**: File(s) listing parts to be used in constructs.
* **Well coordinate for Ethanol**: (string) Coordinates of the well plate providing ethanol for the purification step. Default: A11
-* **Column coordinate for SOC**: (integer) Coordinate of the column plate providing SOC media for the transformation step. Default: 1.
+* **Column coordinate for SOC**: (integer) Coordinate of the column plate providing SOC (Super Optimal broth with Catabolite repression) media for the transformation step. SOC is a nutrient-rich culture media typically used for bacterial transformation. Default: 1.
* **Lab settings file**: Yaml file providing labware IDs and parameter to be used in the Opentrons scripts: `Default settings <https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/dnabot/default_settings.yaml>`_.

diff -r aeebb663a0d9 -r 6dda0879d95a static/images/DNABOT_WF.PNG

Binary file static/images/DNABOT_WF.PNG has changed

diff -r aeebb663a0d9 -r 6dda0879d95a test-data/dnabot_scripts.tar

Binary file test-data/dnabot_scripts.tar has changed