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comparison dnabot.xml @ 2:aeebb663a0d9 draft

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"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author tduigou
date Mon, 04 Apr 2022 15:24:55 +0000
parents de6812daba39
children 6dda0879d95a
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1:de6812daba39 2:aeebb663a0d9
1 <tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="19.09"> 1 <tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="21.09">
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@">3.1.0</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
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" /> 24 <param name="construct_file" type="data" format="csv" label="Source Construct" help="File listing constructs to be implemented."/>
25 <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" /> 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="Yaml file providing labware IDs and parameter to be used" /> 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 name="etoh_well" type="select" label="Well coordinate for Ethanol"> 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>
30 <option value="A3" >A3</option> 30 <option value="A3" >A3</option>
31 <option value="A4" >A4</option> 31 <option value="A4" >A4</option>
32 <option value="A5" >A5</option> 32 <option value="A5" >A5</option>
33 <option value="A6" >A6</option> 33 <option value="A6" >A6</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 name="soc_column" type="select" label="Column coordinate for SOC"> 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.">
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>
52 <option value="12" >12</option> 52 <option value="12" >12</option>
53 </param> 53 </param>
54 </section> 54 </section>
55 </inputs> 55 </inputs>
56 <outputs> 56 <outputs>
57 <data name="dnabot_scripts" format="tar" label="${tool.name} scripts" /> 57 <data name="dnabot_scripts" format="tar" />
58 </outputs> 58 </outputs>
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" />
66 </tests> 66 </tests>
67 <help><![CDATA[ 67 <help><![CDATA[
68 DNA-Bot 68 DNA-Bot
69 ============ 69 ============
70 70
71 DNA assembly using BASIC on OpenTrons 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.
72 72
73 Input 73 Inputs
74 ----- 74 ------
75 75
76 * **default_settings_file**: (string) file providing labware IDs and parameter to be used. Default: dnabot/default_settings.yaml. 76 * **Source Construct**: CSV file listing constructs to be implemented.
77 * **construct_path**: (string) Construct CSV file. 77 * **Plate files**: File(s) listing parts to be used in constructs.
78 * **source_paths**: (string) Source CSV files. 78 * **Well coordinate for Ethanol**: (string) Coordinates of the well plate providing ethanol for the purification step. Default: A11
79 * **etoh_well**: (string) Well coordinate for Ethanol. Default: A11. 79 * **Column coordinate for SOC**: (integer) Coordinate of the column plate providing SOC media for the transformation step. Default: 1.
80 * **soc_column**: (integer) Column coordinate for SOC. 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>`_.
81 * **template_dir**: (string) Template directory. Default: "template_ot2_scripts" located next to the present script. 81
82 82
83 Ouput 83 Ouput
84 ----- 84 -----
85 85
86 * **output_dir**: (string) Output directory. Default: same directory than the one containing the "construct_path" file. 86 * **Dnabot scripts**: DNA-Bot scripts in TAR format which implement the 4 assembly steps and metainformation to keep track of parameters.
87 87
88 Version 88 Version
89 ------- 89 -------
90 90
91 3.1.0 91 3.1.0
97 * Thomas Duigou 97 * Thomas Duigou
98 98
99 License 99 License
100 ------- 100 -------
101 101
102 `MIT <https://github.com/brsynth/DNA-BOT/blob/DNA-BOT-APIv2/LICENSE>`_ 102 `MIT <https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/LICENSE>`_
103 103
104 104
105 Acknowledgments 105 Acknowledgments
106 --------------- 106 ---------------
107 107