diff dnabot.xml @ 0:6d55c77a17ab draft

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dnabot.xml	Tue Dec 14 16:13:36 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>
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