# HG changeset patch
# User iuc
# Date 1510924286 18000
# Node ID 8cc404188faefe1e43d98cea879cfb347d52bef5
# Parent  e738fb9d4a22cfdedc6a0c5395d6150774a6933a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 1672eb3642d19c8502322115b86846297cd5a6b0

diff -r e738fb9d4a22 -r 8cc404188fae minimap2.xml
--- a/minimap2.xml	Wed Nov 08 12:19:49 2017 -0500
+++ b/minimap2.xml	Fri Nov 17 08:11:26 2017 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="minimap2" name="Map with minimap2" version="2.4.1" profile="17.01">
+<tool id="minimap2" name="Map with minimap2" version="2.5" profile="17.01">
     <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
     <requirements>
-        <requirement type="package" version="2.4">minimap2</requirement>
+        <requirement type="package" version="2.5">minimap2</requirement>
         <requirement type="package" version="1.6">samtools</requirement>
     </requirements>
     <version_command>minimap2 --version</version_command>
@@ -89,6 +89,7 @@
     #if $io_options.cs:
         --cs $io_options.cs
     #end if
+    $io_options.Y
     #if $io_options.K:
         -K $io_options.K
     #end if
@@ -211,6 +212,7 @@
                 <option value="short">short</option>
                 <option value="long">long</option>
             </param>
+            <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/>
         </section>
     </inputs>
     <outputs>
diff -r e738fb9d4a22 -r 8cc404188fae test-data/minimap2-test1-fasta.bam
Binary file test-data/minimap2-test1-fasta.bam has changed
diff -r e738fb9d4a22 -r 8cc404188fae test-data/minimap2-test1-fasta.cram
Binary file test-data/minimap2-test1-fasta.cram has changed
diff -r e738fb9d4a22 -r 8cc404188fae test-data/minimap2-test1.bam
Binary file test-data/minimap2-test1.bam has changed
diff -r e738fb9d4a22 -r 8cc404188fae test-data/minimap2-test2.bam
Binary file test-data/minimap2-test2.bam has changed