# HG changeset patch
# User iuc
# Date 1510153315 18000
# Node ID 6090793a47e85cdfb89ca1d4abdd76a37e66fa8f
# Parent  831dcb48efa17000ad4863877268e60dbda96c6c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739

diff -r 831dcb48efa1 -r 6090793a47e8 minimap2.xml
--- a/minimap2.xml	Sat Nov 04 05:40:54 2017 -0400
+++ b/minimap2.xml	Wed Nov 08 10:01:55 2017 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="minimap2" name="Map with minimap2" version="2.3" profile="17.01">
+<tool id="minimap2" name="Map with minimap2" version="2.4" profile="17.01">
     <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
     <requirements>
-        <requirement type="package" version="2.3">minimap2</requirement>
+        <requirement type="package" version="2.4">minimap2</requirement>
         <requirement type="package" version="1.6">samtools</requirement>
     </requirements>
     <version_command>minimap2 --version</version_command>
@@ -429,14 +429,12 @@
 recent samtools will throw an error and abort. Older samtools and other
 tools may create corrupted BAM.
 
-To avoid this issue, you can add option ``-L`` at the minimap2 command
-line. This option moves a long CIGAR to the ``CG`` tag and leaves a
-fully clipped CIGAR at the SAM CIGAR column. Current tools that don’t
-read CIGAR (e.g. merging and sorting) still work with such BAM records;
-tools that read CIGAR will effectively ignore these records. I have pull
-requests to the SAM spec, htslib, htsjdk, bedtools2, Rsamtools and
-igv.js. If they are accepted, future versions of these tools will
-seamlessly recognize long-cigar records generated by option ``-L``.
+To avoid this issue, you can add option ``-L`` at the minimap2 command line.
+This option moves a long CIGAR to the ``CG`` tag and leaves a fully clipped
+CIGAR at the SAM CIGAR column. Current tools that don’t read CIGAR
+(e.g. merging and sorting) still work with such BAM records; tools that read
+CIGAR will effectively ignore these records. It has been decided that future
+tools will seamlessly recognize long-cigar records generated by option `-L`.
 
 **TD;DR**: if you work with ultra-long reads and use tools that only
 process BAM files, please add option ``-L``.
diff -r 831dcb48efa1 -r 6090793a47e8 test-data/minimap2-test1-fasta.bam
Binary file test-data/minimap2-test1-fasta.bam has changed
diff -r 831dcb48efa1 -r 6090793a47e8 test-data/minimap2-test1.bam
Binary file test-data/minimap2-test1.bam has changed
diff -r 831dcb48efa1 -r 6090793a47e8 test-data/minimap2-test2.bam
Binary file test-data/minimap2-test2.bam has changed