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comparison dnabot.xml @ 0:6d55c77a17ab draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 14 Dec 2021 16:13:36 +0000
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1 <tool id="dnabot" name="DNA-Bot" version="3.0.0">
2 <description>DNA assembly using BASIC on OpenTrons</description>
3 <requirements>
4 <requirement type="package" version="3.0.0">dnabot</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 python -m dnabot.dnabot_app
8 #if $adv.default_settings_file
9 --default_settings_file '$adv.default_settings_file'
10 #end if
11 nogui
12 --construct_path '$construct_file'
13 #set files = '" "'.join([str($file) for $file in $plate_files])
14 --source_paths "${files}"
15 --etoh_well '$adv.etoh_well'
16 --soc_column '$adv.soc_column'
17 --output_dir 'output'
18 && tar -cvf '$dnabot_scripts' 'output'
19 ]]></command>
20 <inputs>
21 <param name="construct_file" type="data" format="csv" label="Source Construct" />
22 <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" />
23 <section name="adv" title="Advanced Options" expanded="false">
24 <param name="default_settings_file" type="data" format="yaml" optional="true" label="Yaml file providing labware IDs and parameter to be used" />
25 <param name="etoh_well" type="select" label="Well coordinate for Ethanol">
26 <option value="A2" >A2</option>
27 <option value="A3" >A3</option>
28 <option value="A4" >A4</option>
29 <option value="A5" >A5</option>
30 <option value="A6" >A6</option>
31 <option value="A7" >A7</option>
32 <option value="A8" >A8</option>
33 <option value="A9" >A9</option>
34 <option value="A10" >A10</option>
35 <option value="A11" selected="true">A11</option>
36 </param>
37 <param name="soc_column" type="select" label="Column coordinate for SOC">
38 <option value="1" selected="true">1</option>
39 <option value="2" >2</option>
40 <option value="3" >3</option>
41 <option value="4" >4</option>
42 <option value="5" >5</option>
43 <option value="6" >6</option>
44 <option value="7" >7</option>
45 <option value="8" >8</option>
46 <option value="9" >9</option>
47 <option value="10" >10</option>
48 <option value="11" >11</option>
49 <option value="12" >12</option>
50 </param>
51 </section>
52 </inputs>
53 <outputs>
54 <data name="dnabot_scripts" format="tar" label="${tool.name} scripts" />
55 </outputs>
56 <tests>
57 <test>
58 <!-- test 1: check if identical outputs are produced with compress option -->
59 <param name="construct_file" value="constructs.csv" />
60 <param name="plate_files" value="user_parts_coords.csv,linker_parts_coords.csv"/>
61 <output name="dnabot_scripts" file="dnabot_scripts.tar" compare="sim_size" decompress="True"/>
62 </test>
63 </tests>
64 <help><![CDATA[
65 DNA-Bot
66 ============
67
68 DNA assembly using BASIC on OpenTrons
69
70 Input
71 -----
72
73 * **default_settings_file**: (string) file providing labware IDs and parameter to be used. Default: dnabot/default_settings.yaml.
74 * **construct_path**: (string) Construct CSV file.
75 * **source_paths**: (string) Source CSV files.
76 * **etoh_well**: (string) Well coordinate for Ethanol. Default: A11.
77 * **soc_column**: (integer) Column coordinate for SOC. Default: 1.
78 * **template_dir**: (string) Template directory. Default: "template_ot2_scripts" located next to the present script.
79
80 Ouput
81 -----
82
83 * **output_dir**: (string) Output directory. Default: same directory than the one containing the "construct_path" file.
84
85 Version
86 -------
87
88 3.0.0
89
90 Authors
91 -------
92
93 * **Matthew C Haines**
94 * Thomas Duigou
95
96 License
97 -------
98
99 `MIT <https://github.com/brsynth/DNA-BOT/blob/DNA-BOT-APIv2/LICENSE>`_
100
101
102 Acknowledgments
103 ---------------
104
105 * Marko Storch
106 * Geoff Baldwin
107 ]]></help>
108 <citations>
109 <citation type="bibtex">
110 @article{10.1093/synbio/ysaa010,
111 author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S},
112 title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology},
113 journal = {Synthetic Biology},
114 volume = {5},
115 number = {1},
116 year = {2020},
117 month = {07},
118 issn = {2397-7000},
119 doi = {10.1093/synbio/ysaa010},
120 url = {https://doi.org/10.1093/synbio/ysaa010},
121 note = {ysaa010},
122 eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf},
123 }
124 </citation>
125 </citations>
126 </tool>