# HG changeset patch
# User tduigou
# Date 1652798968 0
# Node ID a2b98a6e033b6353623f8cf89f60ab6c095031ba
# Parent  9603ff31672610efd6c1ee61f98b070fb4780a6c
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"

diff -r 9603ff316726 -r a2b98a6e033b rpbasicdesign.xml
--- a/rpbasicdesign.xml	Fri May 06 16:25:16 2022 +0000
+++ b/rpbasicdesign.xml	Tue May 17 14:49:28 2022 +0000
@@ -1,6 +1,7 @@
-<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09">
+<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
     <description>Build DNA-BOT input files from rpSBML</description>
     <macros>
+        <token name="@VERSION_SUFFIX@">0</token>
         <token name="@TOOL_VERSION@">1.1.0</token>
     </macros>
     <requirements>
@@ -129,18 +130,12 @@
     <help><![CDATA[
 rpbasicdesign
 ================
-
 rpbasicdesign extracts enzyme IDs from rpSBML (System Biology Markup Language) files containing additionnal annotations (e.g. reaction rules ID) and produced by the RP (RetroPath) suite available in `SynBioCAD Galaxy platform <https://galaxy-synbiocad.org/>`_, to generate genetic constructs compliant with the BASIC (Biopart Assembly Standard for Idempotent Cloning) assembly approach. CSV files produced are ready to be used with DNA-Bot to generate instructions for automated build of the genetic constructs using OpenTrons liquid handling robots.
-
 Input
 -----
-
 Required:
-
 * **rpSBML file**\ : rpSBML file from which enzymes UniProt IDs will be collected.
-
 Advanced options:
-
 * **Linkers and user parts**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: ( `Standard Biolegio Parts <https://www.biolegio.com/>`_: BBP-18500).
 * **LMS part ID**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.
 * **LMP part ID**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.
@@ -149,25 +144,18 @@
 * **Perform CDS permutation?**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.
 * **Maximum number of enyzme to consider per reaction**\ : (int) Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept. (Default: 1).
 * **Maximum number of genes per construct**\ : (int) If more genes are required, i.e. more reactions are described in the input SBML file, then the execution will failed. (Default: 3).
-
 Output
 ------
-
 * **constructs**\ : CSV construct file listing the constructs to be built.
 * **User parts plate**\ : CSV file listing the DNA parts to be included into each construct.
 * **Biolegio plate**\ : CSV file listing the plate coordinates of the BASIC linkers.
 * **SBOL constructs**\ : (optional) one SBOL (Synthetic Biology Open Language) file is produced for each construct generated in XML format. 
-
 Project Links
 ------------------
-
 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_
-
 License
 -------
-
 * `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_
-
     ]]></help>
     <citations>
         <citation type="doi">10.1093/synbio/ysaa010</citation>