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comparison dnabot.xml @ 5:21533c69aeac draft

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planemo upload for repository https://github.com/brsynth/DNA-BOT commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
author tduigou
date Mon, 24 Apr 2023 13:23:59 +0000
parents 9dcb6705b80d
children a00a395a6edd
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4:9dcb6705b80d 5:21533c69aeac
19 --soc_column '$adv.soc_column' 19 --soc_column '$adv.soc_column'
20 --output_dir 'output' 20 --output_dir 'output'
21 && tar -cvf '$dnabot_scripts' 'output' 21 && tar -cvf '$dnabot_scripts' 'output'
22 ]]></command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <param name="construct_file" type="data" format="csv" label="Source Construct" help="File listing constructs to be implemented."/> 24 <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)"/>
25 <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" help="File(s) listing parts to be used in constructs." /> 25 <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" help="File(s) listing parts to be used in constructs." />
26 <section name="adv" title="Advanced Options" expanded="false"> 26 <section name="adv" title="Advanced Options" expanded="false">
27 <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." /> 27 <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." />
28 <param argument="--etoh_well" type="select" label="Well coordinate for Ethanol" help="Coordinates of the well plate providing ethanol for the purification step."> 28 <param argument="--etoh_well" type="select" label="Well coordinate for Ethanol" help="Coordinates of the well plate providing ethanol for the purification step.">
29 <option value="A2" >A2</option> 29 <option value="A2" >A2</option>
35 <option value="A8" >A8</option> 35 <option value="A8" >A8</option>
36 <option value="A9" >A9</option> 36 <option value="A9" >A9</option>
37 <option value="A10" >A10</option> 37 <option value="A10" >A10</option>
38 <option value="A11" selected="true">A11</option> 38 <option value="A11" selected="true">A11</option>
39 </param> 39 </param>
40 <param argument="--soc_column" type="select" label="Column coordinate for SOC" help="Coordinate of the column plate providing SOC media for the transformation step."> 40 <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.">
41 <option value="1" selected="true">1</option> 41 <option value="1" selected="true">1</option>
42 <option value="2" >2</option> 42 <option value="2" >2</option>
43 <option value="3" >3</option> 43 <option value="3" >3</option>
44 <option value="4" >4</option> 44 <option value="4" >4</option>
45 <option value="5" >5</option> 45 <option value="5" >5</option>
59 <tests> 59 <tests>
60 <test> 60 <test>
61 <!-- test 1: check if identical outputs are produced with compress option --> 61 <!-- test 1: check if identical outputs are produced with compress option -->
62 <param name="construct_file" value="constructs.csv" /> 62 <param name="construct_file" value="constructs.csv" />
63 <param name="plate_files" value="user_parts_coords.csv,linker_parts_coords.csv"/> 63 <param name="plate_files" value="user_parts_coords.csv,linker_parts_coords.csv"/>
64 <output name="dnabot_scripts" file="dnabot_scripts.tar" compare="sim_size" decompress="True"/> 64 <output name="dnabot_scripts" ftype="tar">
65 <assert_contents>
66 <has_size value="153600" delta="10000"/>
67 </assert_contents>
68 </output>
65 </test> 69 </test>
66 </tests> 70 </tests>
67 <help><![CDATA[ 71 <help><![CDATA[
68 DNA-Bot 72 DNA-Bot
69 ============ 73 ============
70 74
71 **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. 75 **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>`_).
76
77 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.
78
79 .. image:: ${static_path}/images/DNABOT_WF.PNG
80 :width: 90 %
81 :align: center
82
83 |
84
85 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>`_
72 86
73 Inputs 87 Inputs
74 ------ 88 ------
75 89
76 * **Source Construct**: CSV file listing constructs to be implemented. 90 * **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).
77 * **Plate files**: File(s) listing parts to be used in constructs. 91 * **Plate files**: File(s) listing parts to be used in constructs.
78 * **Well coordinate for Ethanol**: (string) Coordinates of the well plate providing ethanol for the purification step. Default: A11 92 * **Well coordinate for Ethanol**: (string) Coordinates of the well plate providing ethanol for the purification step. Default: A11
79 * **Column coordinate for SOC**: (integer) Coordinate of the column plate providing SOC media for the transformation step. Default: 1. 93 * **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.
80 * **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>`_. 94 * **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>`_.
81 95
82 96
83 Ouput 97 Ouput
84 ----- 98 -----