diff lcrgenie.xml @ 0:71568c0c83f4 draft

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

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+++ b/lcrgenie.xml	Mon Dec 20 12:20:40 2021 +0000
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+<tool id="LCRGenie" name="LCR Genie" version="1.0.1">
+    <description>Ligase Chain Reaction</description>
+    <requirements>
+        <requirement type="package" version="1.0.1">lcr_genie</requirement>
+    </requirements>
+    <stdio>
+		<regex match="WARNING:" level="warning" />
+		<regex match="ERROR:" level="fatal" />
+	</stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m lcr_genie
+        '$LCR_input'
+        '$LCR_output'
+        --melting_temp '$adv.melting_temp'
+    ]]></command>
+    <inputs>
+        <param name="LCR_input" type="data" format="xml" label="Constructs" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="melting_temp" value="60.0" type="float" label="Target melting temperature for the bridging oligos" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="LCR_output" format="xlsx" label="LCR Genie: Assembly Plan" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="LCR_input" value="LCR_input_lycopene.xml" />
+            <output name="LCR_output" file="LCR_output_lycopene.xlsx" ftype="xlsx" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+LCRGenie
+========
+
+LCR Genie is a web-based tool for supporting the design of bridging oligos, which are required for annealing together individual synthetic DNA parts (designed by PartsGenie) into multi-gene plasmid assemblies, designed by OptDoE. 
+
+
+Input
+-----
+
+* **input**\ : (string) is the path to an .xml SBOL file containing constructs designs and sequences
+* **melting_temp**\ : (float) is the target melting temperature for the bridging oligos (default=60.0)
+
+Output
+------
+
+* **output**\ : (string) is the path to the output spreadsheet
+
+Project Links
+---------------------
+
+* `GitHub <https://github.com/neilswainston/LCRGenie/>`_
+
+Version
+----------
+
+1.0.1
+
+Authors
+-------
+
+* **Neil Swainston**
+* **Joan Hérisson**
+
+License
+-------
+
+`MIT <https://github.com/neilswainston/LCRGenie/blob/master/LICENSE>`_
+
+
+    ]]></help>
+</tool>