Mercurial > repos > tduigou > dnabot
changeset 2:e6f30afcf8f8 draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Tue, 14 Dec 2021 16:11:38 +0000 |
| parents | c3db8a581ca5 |
| children | 6730c8e1ed09 |
| files | dnabot.xml wrap.xml |
| diffstat | 2 files changed, 126 insertions(+), 126 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dnabot.xml Tue Dec 14 16:11:38 2021 +0000 @@ -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
--- a/wrap.xml Tue Dec 14 14:47:32 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,126 +0,0 @@ -<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="diff" decompress="True" lines_diff="3"/> - </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