# HG changeset patch
# User iuc
# Date 1613070641 0
# Node ID 77b2770508f64673a002fb6ff7b60dd514bd1a77
# Parent  8c6cd2650d1f6eff146db17a1a9e472e98818f3a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89"

diff -r 8c6cd2650d1f -r 77b2770508f6 minimap2.xml
--- a/minimap2.xml	Thu Jun 04 22:29:50 2020 -0400
+++ b/minimap2.xml	Thu Feb 11 19:10:41 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy2" profile="17.01">
+<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy3" profile="17.01">
     <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
     <macros>
         <token name="@TOOL_VERSION@">2.17</token>
@@ -51,7 +51,7 @@
         -f $mapping_options.f
     #end if
     #if str($mapping_options.min_occ_floor):
-        --min-occ-floor $min_occ_floor
+        --min-occ-floor $mapping_options.min_occ_floor
     #end if
     #if str($mapping_options.g):
         -g $mapping_options.g
@@ -440,6 +440,7 @@
         <test>
             <!-- test alignment options -->
             <param name="reference_source_selector" value="cached" />
+            <param name="min_occ_floor" value="1000"/>
             <param name="ref_file" value="bwa-mem-mt-genome"/>
             <param name="fastq_input_selector" value="single"/>
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>