Repository 'minimap2'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/minimap2

Changeset 3:1650a97189be (2017-11-17)
Previous changeset 2:4070f129540a (2017-11-08) Next changeset 4:6f50f36e4481 (2018-08-07)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 1672eb3642d19c8502322115b86846297cd5a6b0
modified:
minimap2.xml
test-data/minimap2-test1-fasta.bam
test-data/minimap2-test1-fasta.cram
test-data/minimap2-test1.bam
test-data/minimap2-test2.bam
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diff -r 4070f129540a -r 1650a97189be minimap2.xml
--- a/minimap2.xml Wed Nov 08 16:48:49 2017 -0500
+++ b/minimap2.xml Fri Nov 17 08:11:42 2017 -0500
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@@ -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>
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diff -r 4070f129540a -r 1650a97189be test-data/minimap2-test1-fasta.bam
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diff -r 4070f129540a -r 1650a97189be test-data/minimap2-test1-fasta.cram
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diff -r 4070f129540a -r 1650a97189be test-data/minimap2-test1.bam
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diff -r 4070f129540a -r 1650a97189be test-data/minimap2-test2.bam
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