| Next changeset 1:de6812daba39 (2022-02-22) |
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Commit message:
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty" |
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added:
dnabot.xml test-data/constructs.csv test-data/dnabot_scripts.tar test-data/linker_parts_coords.csv test-data/user_parts_coords.csv |
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| diff -r 000000000000 -r 6d55c77a17ab dnabot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dnabot.xml Tue Dec 14 16:13:36 2021 +0000 |
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| @@ -0,0 +1,126 @@ +<tool id="dnabot" name="DNA-Bot" version="3.0.0"> + <description>DNA assembly using BASIC on OpenTrons</description> + <requirements> + <requirement type="package" version="3.0.0">dnabot</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python -m dnabot.dnabot_app + #if $adv.default_settings_file + --default_settings_file '$adv.default_settings_file' + #end if + nogui + --construct_path '$construct_file' + #set files = '" "'.join([str($file) for $file in $plate_files]) + --source_paths "${files}" + --etoh_well '$adv.etoh_well' + --soc_column '$adv.soc_column' + --output_dir 'output' + && tar -cvf '$dnabot_scripts' 'output' + ]]></command> + <inputs> + <param name="construct_file" type="data" format="csv" label="Source Construct" /> + <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="default_settings_file" type="data" format="yaml" optional="true" label="Yaml file providing labware IDs and parameter to be used" /> + <param name="etoh_well" type="select" label="Well coordinate for Ethanol"> + <option value="A2" >A2</option> + <option value="A3" >A3</option> + <option value="A4" >A4</option> + <option value="A5" >A5</option> + <option value="A6" >A6</option> + <option value="A7" >A7</option> + <option value="A8" >A8</option> + <option value="A9" >A9</option> + <option value="A10" >A10</option> + <option value="A11" selected="true">A11</option> + </param> + <param name="soc_column" type="select" label="Column coordinate for SOC"> + <option value="1" selected="true">1</option> + <option value="2" >2</option> + <option value="3" >3</option> + <option value="4" >4</option> + <option value="5" >5</option> + <option value="6" >6</option> + <option value="7" >7</option> + <option value="8" >8</option> + <option value="9" >9</option> + <option value="10" >10</option> + <option value="11" >11</option> + <option value="12" >12</option> + </param> + </section> + </inputs> + <outputs> + <data name="dnabot_scripts" format="tar" label="${tool.name} scripts" /> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with compress option --> + <param name="construct_file" value="constructs.csv" /> + <param name="plate_files" value="user_parts_coords.csv,linker_parts_coords.csv"/> + <output name="dnabot_scripts" file="dnabot_scripts.tar" compare="sim_size" decompress="True"/> + </test> + </tests> + <help><![CDATA[ +DNA-Bot +============ + +DNA assembly using BASIC on OpenTrons + +Input +----- + +* **default_settings_file**: (string) file providing labware IDs and parameter to be used. Default: dnabot/default_settings.yaml. +* **construct_path**: (string) Construct CSV file. +* **source_paths**: (string) Source CSV files. +* **etoh_well**: (string) Well coordinate for Ethanol. Default: A11. +* **soc_column**: (integer) Column coordinate for SOC. Default: 1. +* **template_dir**: (string) Template directory. Default: "template_ot2_scripts" located next to the present script. + +Ouput +----- + +* **output_dir**: (string) Output directory. Default: same directory than the one containing the "construct_path" file. + +Version +------- + +3.0.0 + +Authors +------- + +* **Matthew C Haines** +* Thomas Duigou + +License +------- + +`MIT <https://github.com/brsynth/DNA-BOT/blob/DNA-BOT-APIv2/LICENSE>`_ + + +Acknowledgments +--------------- + +* Marko Storch +* Geoff Baldwin + ]]></help> + <citations> + <citation type="bibtex"> + @article{10.1093/synbio/ysaa010, + author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S}, + title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology}, + journal = {Synthetic Biology}, + volume = {5}, + number = {1}, + year = {2020}, + month = {07}, + issn = {2397-7000}, + doi = {10.1093/synbio/ysaa010}, + url = {https://doi.org/10.1093/synbio/ysaa010}, + note = {ysaa010}, + eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf}, + } + </citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 6d55c77a17ab test-data/constructs.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constructs.csv Tue Dec 14 16:13:36 2021 +0000 |
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| @@ -0,0 +1,4 @@ +Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 +A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS2,D5AP78,U3-RBS3,Q1XBU4,U2-RBS1,O66129,,,,,,,,,, +A2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,D2WKD9,U2-RBS3,O48935,U3-RBS1,O66952,,,,,,,,,, +A3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS2,P48537,U3-RBS2,O07333,U1-RBS2,Q9C446,,,,,,,,,, |
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| diff -r 000000000000 -r 6d55c77a17ab test-data/dnabot_scripts.tar |
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| Binary file test-data/dnabot_scripts.tar has changed |
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| diff -r 000000000000 -r 6d55c77a17ab test-data/linker_parts_coords.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/linker_parts_coords.csv Tue Dec 14 16:13:36 2021 +0000 |
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| @@ -0,0 +1,83 @@ +Part/linker,Well,Part concentration (ng/uL) +L1-S,A1, +L1-P,B1, +L2-S,A2, +L2-P,B2, +L3-S,A3, +L3-P,B3, +L4-S,A4, +L4-P,B4, +L5-S,A5, +L5-P,B5, +L6-S,A6, +L6-P,B6, +LMP-S,A7, +LMP-P,B7, +LMS-S,A8, +LMS-P,B8, +U1-S,C1, +U2-S,C2, +U3-S,C3, +U1-RBS1-P,C4, +U1-RBS2-P,C5, +U1-RBS3-P,C6, +U1-A01-P,D1, +U1-A02-P,D2, +U1-A03-P,D3, +U1-A04-P,D4, +U1-A05-P,D5, +U1-A06-P,D6, +U1-A07-P,D7, +U1-A08-P,D8, +U1-A09-P,D9, +U1-A10-P,D10, +U1-A11-P,D11 +U1-A12-P,D12, +U2-RBS1-P,C7, +U2-RBS2-P,C8, +U2-RBS3-P,C9, +U2-A01-P,E1, +U2-A02-P,E2, +U2-A03-P,E3, +U2-A04-P,E4, +U2-A05-P,E5, +U2-A06-P,E6, +U2-A07-P,E7, +U2-A08-P,E8, +U2-A09-P,E9, +U2-A10-P,E10, +U2-A11-P,E11 +U2-A12-P,E12, +U3-RBS1-P,C10, +U3-RBS2-P,C11, +U3-RBS3-P,C12, +U3-A01-P,F1, +U3-A02-P,F2, +U3-A03-P,F3, +U3-A04-P,F4, +U3-A05-P,F5, +U3-A06-P,F6, +U3-A07-P,F7, +U3-A08-P,F8, +U3-A09-P,F9, +U3-A10-P,F10, +U3-A11-P,F11 +U3-A12-P,F12, +U1-AM12-P,A10, +U1-AM24-P,B10, +U2-AM12-P,A11, +U2-AM24-P,B11, +U3-AM12-P,A12, +U3-AM24-P,B12, +LF1-S,A9, +LF1-P,B9, +LF2-S,G1, +LF2-P,H1, +LF3-S,G2, +LF3-P,H2, +LF4-S,G3, +LF4-P,H3, +LF5-S,G4, +LF5-P,H4, +LF6-S,G5, +LF6-P,H5, \ No newline at end of file |
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| diff -r 000000000000 -r 6d55c77a17ab test-data/user_parts_coords.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/user_parts_coords.csv Tue Dec 14 16:13:36 2021 +0000 |
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| @@ -0,0 +1,13 @@ +Part/linker,Well,Part concentration (ng/uL) +BASIC_SEVA_37_CmR-p15A.1,A1, +D2WKD9,A2, +D5AP78,A3, +O07333,A4, +O48935,A5, +O66129,A6, +O66952,A7, +P48537,A8, +PJ23101_BASIC,A9, +PJ23104_BASIC,A10, +Q1XBU4,A11, +Q9C446,A12, |