Mercurial > repos > iuc > dnabot

annotate dnabot.xml @ 0:6183de71c59e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
author iuc
date Tue, 17 May 2022 13:27:06 +0000
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0
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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1 <tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="21.09">
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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2 <description>DNA assembly using BASIC on OpenTrons</description>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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3 <macros>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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4 <token name="@TOOL_VERSION@">3.1.0</token>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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5 </macros>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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6 <requirements>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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7 <requirement type="package" version="@TOOL_VERSION@">dnabot</requirement>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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8 </requirements>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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9 <command detect_errors="exit_code"><![CDATA[
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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10 python -m dnabot.dnabot_app
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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11 #if $adv.default_settings_file
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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12 --default_settings_file '$adv.default_settings_file'
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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13 #end if
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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14 nogui
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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15 --construct_path '$construct_file'
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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16 #set files = '" "'.join([str($file) for $file in $plate_files])
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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17 --source_paths "${files}"
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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18 --etoh_well '$adv.etoh_well'
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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19 --soc_column '$adv.soc_column'
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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20 --output_dir 'output'
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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21 && tar -cvf '$dnabot_scripts' 'output'
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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22 ]]></command>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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23 <inputs>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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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)"/>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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25 <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" help="File(s) listing parts to be used in constructs." />
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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26 <section name="adv" title="Advanced Options" expanded="false">
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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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." />
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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28 <param argument="--etoh_well" type="select" label="Well coordinate for Ethanol" help="Coordinates of the well plate providing ethanol for the purification step.">
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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29 <option value="A2" >A2</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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30 <option value="A3" >A3</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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31 <option value="A4" >A4</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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32 <option value="A5" >A5</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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33 <option value="A6" >A6</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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34 <option value="A7" >A7</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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35 <option value="A8" >A8</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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36 <option value="A9" >A9</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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37 <option value="A10" >A10</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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38 <option value="A11" selected="true">A11</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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39 </param>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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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.">
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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41 <option value="1" selected="true">1</option>
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42 <option value="2" >2</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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43 <option value="3" >3</option>
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44 <option value="4" >4</option>
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45 <option value="5" >5</option>
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46 <option value="6" >6</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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47 <option value="7" >7</option>
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48 <option value="8" >8</option>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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49 <option value="9" >9</option>
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50 <option value="10" >10</option>
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51 <option value="11" >11</option>
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52 <option value="12" >12</option>
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53 </param>
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54 </section>
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55 </inputs>
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56 <outputs>
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57 <data name="dnabot_scripts" format="tar" />
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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58 </outputs>
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59 <tests>
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60 <test>
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61 <!-- test 1: check if identical outputs are produced with compress option -->
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62 <param name="construct_file" value="constructs.csv" />
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63 <param name="plate_files" value="user_parts_coords.csv,linker_parts_coords.csv"/>
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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64 <output name="dnabot_scripts" ftype="tar">
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65 <assert_contents>
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66 <has_size value="153600" delta="10000"/>
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67 </assert_contents>
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68 </output>
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72 DNA-Bot
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73 ============
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74
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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>`_).
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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76
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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.
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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78
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79 .. image:: ${static_path}/images/DNABOT_WF.PNG
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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80 :width: 90 %
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81 :align: center
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82
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83 |
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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84
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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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>`_
6183de71c59e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot commit 26909099e5c61564bd72f67974e30e75f3fad22c
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86
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87 Inputs
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88 ------
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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).
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91 * **Plate files**: File(s) listing parts to be used in constructs.
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92 * **Well coordinate for Ethanol**: (string) Coordinates of the well plate providing ethanol for the purification step. Default: A11
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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.
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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>`_.
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96
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97 Ouput
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98 -----
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99
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100 * **Dnabot scripts**: DNA-Bot scripts in TAR format which implement the 4 assembly steps and metainformation to keep track of parameters.
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101
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102 Version
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103 -------
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104
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105 3.1.0
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106
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107 Authors
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108 -------
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109
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110 * **Matthew C Haines**
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111 * Thomas Duigou
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112
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113 License
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114 -------
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115
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116 `MIT <https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/LICENSE>`_
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118
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119 Acknowledgments
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120 ---------------
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121
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122 * Marko Storch
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123 * Geoff Baldwin
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124 ]]></help>
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125 <citations>
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126 <citation type="doi">10.1093/synbio/ysaa010</citation>
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127 </citations>
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128 </tool>