diff basil.xml @ 2:bf1bdb62d882 draft default tip

planemo upload commit beceb2f899abad7217eb72f57f6985c4ad4c17a8

--- a/basil.xml	Sun Aug 11 21:06:14 2024 +0000
+++ b/basil.xml	Fri Jul 18 08:43:41 2025 +0000
@@ -2,7 +2,7 @@
     <description>Breakpoint detection, including large insertions</description>
     <macros>
         <token name="@TOOL_VERSION@">1.2.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">anise_basil</requirement>
@@ -38,7 +38,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="ref" argument="--input-reference" type="data" format="Fasta" label="Reference Sequence File" help="FASTA file with the reference."/>
+                <param name="ref" argument="--input-reference" type="data" format="fasta" label="Reference Sequence File" help="FASTA file with the reference."/>
             </when>
         </conditional>
         <param name="bam" argument="--input-mapping" type="data" format="sam,bam" label="Alignment File" help="SAM/BAM file to use as the input."/>
@@ -53,7 +53,6 @@
                 <param name="reference_source_selector" value="history" />
                 <param name="ref" ftype="fasta" value="ref.fa"/>
             </conditional>
-            <param name="ref" value="ref.fa"/>
             <param name="bam" value="simulated.bam"/>
             <param name="min_oea_each_side" value="2"/>
             <output name="vcf" file="basil.vcf"/>