diff tbvcfreport.xml @ 3:42818629ec4c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17

--- a/tbvcfreport.xml	Thu Mar 17 07:33:00 2022 +0000
+++ b/tbvcfreport.xml	Fri May 31 20:06:49 2024 +0000
@@ -1,8 +1,8 @@
 <?xml version="1.0" ?>
-<tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0">
+<tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="AGPL-3.0-or-later">
   <description>- generate HTML report from SnpEff annotated M.tb VCF(s)</description>
   <macros>
-    <token name="@TOOL_VERSION@">0.1.10</token>
+    <token name="@TOOL_VERSION@">1.0.0</token>
   </macros>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement>
@@ -62,7 +62,7 @@
   <inputs>
     <param name="input_vcf" type="data" format="vcf" label="Input SnpEff annotated M.tuberculosis VCF(s)" />
     <param name="tbprofiler_json" type="data" format="json" optional="true" label="TBProfiler Drug Resistance Report (Optional)" help="--tbprofiler-report" />
-    <param name="filter_udi" argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" />
+    <param argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" />
     <section name="adv" title="Advanced options" expanded="false">
       <param name="database_uri" type="text" optional="true" value="neodb.sanbi.ac.za" label="Specify COMBAT-TB-NeoDB URI" help="For people with their own deployment of COMBAT-TB-NeoDB" />
     </section>
@@ -102,7 +102,7 @@
     <![CDATA[
     **tbvcfreport - @TOOL_VERSION@**
 
-    **tbvcfreport** takes SnpEff annotated M.tuberculosis VCF file(s) and generates an HTML-based report with data from Combat-TB-NeoDB (https://neodb.sanbi.ac.za) 
+    **tbvcfreport** takes SnpEff annotated M.tuberculosis VCF file(s) and generates an HTML-based report with data from Combat-TB-NeoDB  
     and links to Combat-TB-eXplorer (https://explorer.sanbi.ac.za/).
 
     **tbvcfreport** will generate an HTML-based Drug Resistance report if provided with a TBProfiler json report.