changeset 1:e73c927dc332 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign commit b4fb63a436c6c8711bacb4f35c1eab17a17efd16

--- a/rpbasicdesign.xml	Wed Mar 30 13:05:31 2022 +0000
+++ b/rpbasicdesign.xml	Mon May 23 10:56:05 2022 +0000
@@ -1,7 +1,8 @@
-<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="@TOOL_VERSION@">1.0.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@TOOL_VERSION@">1.1.0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement>
@@ -21,6 +22,7 @@
         --o_dnabot_dir 'out/dnabot_in'
         $adv.sbol_output
         --max_enz_per_rxn $adv.max_enz_per_rxn
+        --max_gene_per_construct $adv.max_gene_per_construct
     ]]></command>
     <inputs>
         <param name="rpsbml_file" type="data" format="sbml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/>
@@ -35,7 +37,7 @@
             </sanitizer>
             <validator type="empty_field" message="Backbone ID is required"/>
         </param>
-        <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Sample size" help="Number of constructs to generate."/>
+        <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Sample size" help="Number of construct to generate."/>
         <section name="adv" title="Advanced Options" expanded="false">
             <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" help="List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: Standard Biolegio Parts (BBP-18500)" />
             <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." >
@@ -63,6 +65,7 @@
             <param argument="--cds_permutation" type="boolean" truevalue="--cds_permutation true" falsevalue="--cds_permutation false" checked="true" label="Perform CDS permutation?" help="Whether all combinations of CDS permutation should be built." />
             <param argument="--sbol_output" type="boolean" checked="false" truevalue="--o_sbol_dir out/sbol_export" falsevalue="" label="Output SBOL results?" help="Whether SBOL (Synthetic Biology Open Language) depictions of constructs should be outputted" />
             <param argument="--max_enz_per_rxn" type="integer" value="1" min="1" max="99" label="Maximum number of enyzme to consider per reaction." help="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."/>
+            <param argument="--max_gene_per_construct" type="integer" value="3" min="1" max="10" label="Maximum number of genes per construct" help="If more genes are required, i.e. more reactions are described in the input SBML file, then the execution will failed."/>
         </section>
     </inputs>
     <outputs>
@@ -143,9 +146,10 @@
 * **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.
 * **Backbone part ID**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.
-* **Sample size**\ : (int) Number of constructs to generate. Default: 88.
+* **Sample size**\ : (int) Number of construct to generate. Default: 88.
 * **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 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
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