# HG changeset patch
# User tduigou
# Date 1649085895 0
# Node ID aeebb663a0d990180ac46643ea7152f252c60390
# Parent  de6812daba39eaacf73d5659e268c5cfe7a06596
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"

diff -r de6812daba39 -r aeebb663a0d9 dnabot.xml
--- a/dnabot.xml	Tue Feb 22 13:43:44 2022 +0000
+++ b/dnabot.xml	Mon Apr 04 15:24:55 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="19.09">
+<tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="21.09">
     <description>DNA assembly using BASIC on OpenTrons</description>
     <macros>
         <token name="@TOOL_VERSION@">3.1.0</token>
@@ -21,11 +21,11 @@
         && 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" />
+        <param name="construct_file" type="data" format="csv" label="Source Construct" help="File listing constructs to be implemented."/>
+        <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" help="File(s) listing parts to be used in constructs." />
         <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">
+            <param name="default_settings_file" type="data" format="yaml" optional="true" label="Lab settings file" help="Yaml file providing labware IDs and parameter to be used in the Opentrons scripts." />
+            <param argument="--etoh_well" type="select" label="Well coordinate for Ethanol" help="Coordinates of the well plate providing ethanol for the purification step.">
                 <option value="A2" >A2</option>
                 <option value="A3" >A3</option>
                 <option value="A4" >A4</option>
@@ -37,7 +37,7 @@
                 <option value="A10" >A10</option>
                 <option value="A11" selected="true">A11</option>
             </param>
-            <param name="soc_column" type="select" label="Column coordinate for SOC">
+            <param argument="--soc_column" type="select" label="Column coordinate for SOC" help="Coordinate of the column plate providing SOC media for the transformation step."> 
                 <option value="1" selected="true">1</option>
                 <option value="2" >2</option>
                 <option value="3" >3</option>
@@ -54,7 +54,7 @@
         </section>
     </inputs>
     <outputs>
-        <data name="dnabot_scripts" format="tar" label="${tool.name} scripts" />
+        <data name="dnabot_scripts" format="tar" />
     </outputs>
     <tests>
         <test>
@@ -68,22 +68,22 @@
 DNA-Bot
 ============
 
-DNA assembly using BASIC on OpenTrons
+ **DNA-Bot** tool reads the list of constructs (previously produced by `rpBasicDesign <https://toolshed.g2.bx.psu.edu/view/iuc/rpbasicdesign/cdd6a526bdcf>`_) and the DNA-parts position on the source plates and generates a set of python scripts to drive an Opentrons liquid handling robot for building the plasmids using BASIC assembly method (as decribed in `Storch2015 <https://doi.org/10.1021/sb500356d>`_). Optional parameters can be set by the user to define the plastic labwares to be used, and set protocol parameters such as washing or incubation times for purification step by providing a YAML settings file.
 
-Input
------
+Inputs
+------
 
-* **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.
+* **Source Construct**: CSV file listing constructs to be implemented.
+* **Plate files**: File(s) listing parts to be used in constructs.
+* **Well coordinate for Ethanol**: (string) Coordinates of the well plate providing ethanol for the purification step. Default: A11
+* **Column coordinate for SOC**: (integer) Coordinate of the column plate providing SOC media for the transformation step. Default: 1.
+* **Lab settings file**: Yaml file providing labware IDs and parameter to be used in the Opentrons scripts: `Default settings <https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/dnabot/default_settings.yaml>`_.
+
 
 Ouput
 -----
 
-* **output_dir**: (string) Output directory. Default: same directory than the one containing the "construct_path" file.
+* **Dnabot scripts**: DNA-Bot scripts in TAR format which implement the 4 assembly steps and metainformation to keep track of parameters.
 
 Version
 -------
@@ -99,7 +99,7 @@
 License
 -------
 
-`MIT <https://github.com/brsynth/DNA-BOT/blob/DNA-BOT-APIv2/LICENSE>`_
+`MIT <https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/LICENSE>`_
 
 
 Acknowledgments