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comparison dnabot.xml @ 7:ecb31af4c2f8 draft default tip

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planemo upload for repository https://github.com/brsynth/DNA-BOT commit 79f27123846add7020de9cae2912e5289c2b8efd
author tduigou
date Tue, 23 Jul 2024 09:55:58 +0000
parents ec9cef4b5b5a
children
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6:ec9cef4b5b5a 7:ecb31af4c2f8
1 <tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="21.09" license="MIT"> 1 <tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="21.09" license="MIT">
2 <description>DNA assembly using BASIC on OpenTrons</description> 2 <description>DNA assembly using BASIC on OpenTrons</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">3.1.0</token> 4 <token name="@TOOL_VERSION@">4.1.0</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">dnabot</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">dnabot</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
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" ftype="tar"> 64 <output name="dnabot_scripts" ftype="tar">
65 <assert_contents> 65 <assert_contents>
66 <has_size value="150000" delta="10000"/> 66 <has_size value="160000" delta="10000"/>
67 </assert_contents> 67 </assert_contents>
68 </output> 68 </output>
69 </test> 69 </test>
70 </tests> 70 </tests>
71 <help><![CDATA[ 71 <help><![CDATA[
72 DNA-Bot 72 DNA-Bot
73 ============ 73 ============
74 74
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>`_). 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 by Storch et al. (10.1021/sb500356d).
76 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. 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 78
79 .. image:: ${static_path}/images/DNABOT_WF.PNG 79 .. image:: ${static_path}/images/DNABOT_WF.PNG
80 :width: 90 % 80 :width: 90 %