# HG changeset patch
# User iuc
# Date 1586299178 14400
# Node ID 53c0b7a1a0c395a560dfe5f7af2a48c3e356cbc8
# Parent  b3eab4b675624b2f59b84c582753d20dd29004bf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba"

diff -r b3eab4b67562 -r 53c0b7a1a0c3 minimap2.xml
--- a/minimap2.xml	Fri Oct 11 13:27:18 2019 -0400
+++ b/minimap2.xml	Tue Apr 07 18:39:38 2020 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy0" profile="17.01">
+<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy1" profile="17.01">
     <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
     <macros>
         <token name="@TOOL_VERSION@">2.17</token>
@@ -97,6 +97,7 @@
     ## Output options
     $io_options.Q
     $io_options.L
+    $io_options.c
     #if $io_options.cs:
         --cs $io_options.cs
     #end if
@@ -183,16 +184,16 @@
         </conditional>
         <!-- end unchanged copy from bwa-mem -->
         <param name="analysis_type_selector" type="select" label="Select analysis mode (sets default)">
-            <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19)</option>
-            <option value="map-ont">Oxford Nanopore read to reference mapping. Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For PacBio reads, HPC minimizers consistently leads to faster performance and more sensitive results in comparison to normal minimizers. For Oxford Nanopore data, normal minimizers are better, though not much. The effectiveness of HPC is determined by the sequencing error mode.</option>
-            <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25)</option>
-            <option value="ava-ont">Oxford Nanopore all-vs-all overlap mapping (-k15 -Xw5 -m100 -g10000 -r2000 --max-chain-skip 25). Similarly, the major difference from ava-pb is that this preset is not using HPC minimizers.</option>
-            <option value="asm5">Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%.</option>
-            <option value="asm10">Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 10% sequence divergence.</option>
-            <option value="asm20">Long assembly to reference mapping (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence.</option>
-            <option value="splice">Long-read spliced alignment (-k15 -w5 --splice -g2000 -G200k  -A1 -B2  -O2,32  -E1,0  -C9  -z200  -ub  --splice-flank=yes). In the splice mode, 1) long deletions are taken as  introns  and  represented as the `N' CIGAR operator 2) long insertions are disabled 3) deletion and insertion gap costs are different during chaining 4) the computation of the `ms' tag ignores introns to demote hits to pseudogenes.</option>
-            <option value="sr">Short single-end reads without splicing (-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no)</option>
-            <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200)</option>
+            <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19) (map-pb)</option>
+            <option value="map-ont">Oxford Nanopore read to reference mapping. Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For PacBio reads, HPC minimizers consistently leads to faster performance and more sensitive results in comparison to normal minimizers. For Oxford Nanopore data, normal minimizers are better, though not much. The effectiveness of HPC is determined by the sequencing error mode. (map-ont)</option>
+            <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25) (ava-pb)</option>
+            <option value="ava-ont">Oxford Nanopore all-vs-all overlap mapping (-k15 -Xw5 -m100 -g10000 -r2000 --max-chain-skip 25). Similarly, the major difference from ava-pb is that this preset is not using HPC minimizers. (ava-ont)</option>
+            <option value="asm5">Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%. (asm5)</option>
+            <option value="asm10">Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 10% sequence divergence. (asm10)</option>
+            <option value="asm20">Long assembly to reference mapping (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence. (asm20)</option>
+            <option value="splice">Long-read spliced alignment (-k15 -w5 --splice -g2000 -G200k  -A1 -B2  -O2,32  -E1,0  -C9  -z200  -ub  --splice-flank=yes). In the splice mode, 1) long deletions are taken as  introns  and  represented as the `N' CIGAR operator 2) long insertions are disabled 3) deletion and insertion gap costs are different during chaining 4) the computation of the `ms' tag ignores introns to demote hits to pseudogenes. (splice)</option>
+            <option value="sr">Short single-end reads without splicing (-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option>
+            <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200) (self-homology)</option>
         </param>
         <section name="mapping_options" title="Set advanced mapping options" help="Sets -f, -g, -G, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False">
             <param argument="-f" type="float" value="" optional="true" label="filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
@@ -228,14 +229,17 @@
                 <option value="CRAM">CRAM</option>
                 <option value="paf">paf</option>
             </param>
-            <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" optional="true" label="don't output base quality"/>
-            <param argument="-L" type="boolean" truevalue="-L" falsevalue="" optional="true" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/>
+            <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" label="don't output base quality"/>
+            <param argument="-L" type="boolean" truevalue="-L" falsevalue="" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/>
             <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/>
             <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below.">
                 <option value="none">no</option>
                 <option value="short">short</option>
                 <option value="long">long</option>
             </param>
+            <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Generate CIGAR"
+                help="In PAF, the CIGAR is written to the ‘cg’ custom tag." />
+
             <param argument="--eqx" type="boolean" truevalue="--eqx" falsevalue="" label="write =/X CIGAR operators"/>
             <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/>
         </section>