# HG changeset patch
# User tduigou
# Date 1639498416 0
# Node ID 6d55c77a17ab432c70e995af3ed12a1d0770e07c

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

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
@@ -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
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
@@ -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,,,,,,,,,,
diff -r 000000000000 -r 6d55c77a17ab test-data/dnabot_scripts.tar
Binary file test-data/dnabot_scripts.tar has changed
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
@@ -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
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
@@ -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,