minimap2: minimap2.xml annotate

annotate minimap2.xml @ 15:6d5a7cc63314 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba"

author	iuc
date	Tue, 07 Apr 2020 22:39:16 +0000
parents	4f88b74199bf
children	fd3673a18ad3

rev	line source
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	1 <?xml version="1.0"?>
15 6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy1" profile="17.01">
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	4 <macros>
13 ba69511b9e66 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 0eca6ecb53be7fb0050b6671d0efe03d79247229 iuc parents: 12 diff changeset	5 <token name="@TOOL_VERSION@">2.17</token>
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	6 </macros>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	7 <requirements>
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	8 <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement>
440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	9 <requirement type="package" version="1.9">samtools</requirement>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	10 </requirements>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	11 <version_command>minimap2 --version</version_command>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	12 <command>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	13 <![CDATA[
5 3875e9b17ca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: 4 diff changeset	14 #if $reference_source.reference_source_selector == 'history':
3 acb6d016cabe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: 0 diff changeset	15 ln -f -s '$reference_source.ref_file' reference.fa &&
acb6d016cabe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: 0 diff changeset	16 #else:
6 4d84d86b368e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: 5 diff changeset	17 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
4 cd71cf88d971 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: 3 diff changeset	18 #end if
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	19 minimap2
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	20 #if str($analysis_type_selector) == 'self-homology':
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	21 -DP -k19 -w19 -m200
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	22 #else
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	23 -x $analysis_type_selector
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	24 #end if
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	25 ## indexing options
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	26 $indexing_options.H
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	27 #if $indexing_options.k:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	28 -k $indexing_options.k
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	29 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	30 #if $indexing_options.w:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	31 -w $indexing_options.w
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	32 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	33 #if $indexing_options.I:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	34 -I $indexing_options.I
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	35 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	36 ## Mapping options
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	37 #if $mapping_options.f:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	38 -f $mapping_options.f
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	39 #end if
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	40 #if $mapping_options.min_occ_floor:
440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	41 --min-occ-floor $min_occ_floor
440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	42 #end if
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	43 #if $mapping_options.g:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	44 -g $mapping_options.g
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	45 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	46 #if $mapping_options.G:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	47 -G $mapping_options.G
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	48 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	49 #if $mapping_options.F:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	50 -F $mapping_options.F
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	51 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	52 #if $mapping_options.r:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	53 -r $mapping_options.r
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	54 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	55 #if $mapping_options.n:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	56 -n $mapping_options.n
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	57 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	58 #if $mapping_options.m:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	59 -m $mapping_options.m
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	60 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	61 $mapping_options.X
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	62 #if $mapping_options.p:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	63 -p $mapping_options.p
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	64 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	65 #if $mapping_options.N:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	66 -N $mapping_options.N
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	67 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	68 ## Alignment options
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	69 #if $alignment_options.A:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	70 -A $alignment_options.A
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	71 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	72 #if $alignment_options.B:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	73 -B $alignment_options.B
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	74 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	75 #if $alignment_options.O:
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	76 #if $alignment_options.O2:
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	77 -O $alignment_options.O,$alignment_options.O2
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	78 #end if
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	79 -O $alignment_options.O
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	80 #end if
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	81 #if $alignment_options.E:
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	82 #if $alignment_options.E2:
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	83 -E $alignment_options.E,$alignment_options.E2
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	84 #else
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	85 -E $alignment_options
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	86 #end if
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	87 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	88 #if $alignment_options.z:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	89 $alignment_options.z
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	90 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	91 #if $alignment_options.s:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	92 -s $alignment_options.s
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	93 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	94 #if $alignment_options.u:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	95 -u $alignment_options.u
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	96 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	97 ## Output options
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	98 $io_options.Q
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	99 $io_options.L
15 6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	100 $io_options.c
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	101 #if $io_options.cs:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	102 --cs $io_options.cs
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	103 #end if
10 8cc404188fae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 1672eb3642d19c8502322115b86846297cd5a6b0 iuc parents: 9 diff changeset	104 $io_options.Y
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	105 #if $io_options.K:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	106 -K $io_options.K
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	107 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	108 -t \${GALAXY_SLOTS:-4}
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	109 reference.fa
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	110 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	111 '$fastq_input.fastq_input1'
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	112 #else if $fastq_input.fastq_input_selector == 'paired':
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	113 '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	114 #else if $fastq_input.fastq_input_selector == 'paired_collection':
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	115 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	116 #end if
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	117 #if $io_options.output_format == 'BAM':
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	118 -a
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	119 \| samtools sort
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	120 -@\${GALAXY_SLOTS:-2}
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	121 -T "\${TMPDIR:-.}"
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	122 -O $io_options.output_format
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	123 -o '$alignment_output'
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	124 #else if $io_options.output_format == 'CRAM':
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	125 -a
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	126 \| samtools sort
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	127 -T "\${TMPDIR:-.}"
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	128 -@\${GALAXY_SLOTS:-2}
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	129 -O $io_options.output_format
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	130 $io_options.eqx
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	131 --reference reference.fa
9 e738fb9d4a22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ba952bea405513c0d81a33019a4c2fbcdcf8e783 iuc parents: 8 diff changeset	132 --output-fmt-option no_ref
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	133 -o '$alignment_output'
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	134 #end if
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	135 > '$alignment_output'
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	136 ]]>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	137 </command>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	138 <inputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	139 <conditional name="reference_source">
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	140 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	141 <option value="cached">Use a built-in genome index</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	142 <option value="history">Use a genome from history and build index</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	143 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	144 <when value="cached">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	145 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	146 <options from_data_table="all_fasta">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	147 <filter type="sort_by" column="2" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	148 <validator type="no_options" message="No reference genomes are available" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	149 </options>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	150 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	151 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	152 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	153 <when value="history">
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	154 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	155 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	156 </conditional>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	157 <section name="indexing_options" title="Indexing options">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	158 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	159 <param argument="-k" type="integer" min="4" max="28" optional="true" label="k-mer size" help=""/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	160 <param argument="-w" type="integer" min="1" optional="true" label="minimizer window size" help=""/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	161 <param argument="-I" type="integer" min="1" optional="true" label="split index for every N input gigabases" help=""/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	162 </section>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	163 <!-- start unchanged copy from bwa-mem -->
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	164 <conditional name="fastq_input">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	165 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	166 <option value="single">Single</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	167 <option value="paired">Paired</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	168 <option value="paired_collection">Paired Collection</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	169 <option value="paired_iv">Paired Interleaved</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	170 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	171 <when value="paired">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	172 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	173 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	174 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	175 <when value="single">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	176 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	177 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	178 <when value="paired_collection">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	179 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	180 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	181 <when value="paired_iv">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	182 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	183 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	184 </conditional>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	185 <!-- end unchanged copy from bwa-mem -->
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	186 <param name="analysis_type_selector" type="select" label="Select analysis mode (sets default)">
15 6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	187 <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19) (map-pb)</option>
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	188 <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>
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	189 <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25) (ava-pb)</option>
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	190 <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>
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	191 <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>
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	192 <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>
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	193 <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>
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	194 <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>
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	195 <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>
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	196 <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200) (self-homology)</option>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	197 </param>
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	198 <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">
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	199 <param argument="-f" type="float" value="" optional="true" label="filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	200 <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="force minimap2 to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	201 <param argument="-g" type="integer" value="" optional="true" label="stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	202 <param argument="-G" type="integer" value="" optional="true" label="max intron length in thousand (effective with -xsplice; changing -r)" help="default=200"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	203 <param argument="-F" type="integer" value="" optional="true" label="max fragment length (effective with -xsr or in the fragment mode)" help="default=800" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	204 <param argument="-r" type="integer" value="" optional="true" label="bandwidth used in chaining and DP-based alignment" help="default=500" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	205 <param argument="-n" type="integer" value="" optional="true" label="minimal number of minimizers on a chain" help="default=3"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	206 <param argument="-m" type="integer" value="" optional="true" label="minimal chaining score (matching bases minus log gap penalty)" help="default=40"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	207 <param argument="-X" type="boolean" truevalue="-X" falsevalue="" optional="true" label="skip self and dual mappings (for the all-vs-all mode)"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	208 <param argument="-p" type="float" value="" max="1" optional="true" label="min secondary-to-primary score ratio" help="default=0.8"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	209 <param argument="-N" type="integer" min="0" optional="true" label="retain at most INT secondary alignments" help="default=5"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	210 </section>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	211 <section name="alignment_options" title="Set advanced alignment options" help="Sets -A, -B, -O, -E, -z, -s and -u options." expanded="False">
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	212 <param argument="-A" type="integer" optional="true" label="Score for a sequence match" help="default=2"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	213 <param argument="-B" type="integer" optional="true" label="Penalty for a mismatch" help="-B; default=4" />
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	214 <param argument="-O" type="integer" min="0" optional="true" label="Gap open penalties for deletions" help="-O; default=4"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	215 <param name="-O2" type="integer" min="0" optional="true" label="Gap open penalties for insertions" help="-O; default=24"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	216 <param argument="-E" type="integer" min="0" optional="true" label="Gap extension penalties; a gap of size k cost '-O + -E*k'. If two numbers are specified, the first is the penalty of extending a deletion and the second for extending an insertion" help="-E; default=2"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	217 <param name="E2" type="integer" min="0" optional="true" label="Gap extension penalty for extending an insertion; if left empty uses the value specified for Gap extension penalties above" help="-E; default=1"/>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	218 <param argument="-z" type="integer" optional="true" label="Z-drop score" help="default=400"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	219 <param argument="-s" type="integer" optional="true" label="minimal peak DP alignment score" help="default=80"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	220 <param argument="-u" type="select" optional="true" label="how to find GT-AG">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	221 <option value="n">don't match GT-AG</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	222 <option value="f">transcript strand</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	223 <option value="b">both strands</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	224 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	225 </section>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	226 <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False">
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	227 <param name="output_format" type="select" label="Select an output format">
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	228 <option value="BAM">BAM</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	229 <option value="CRAM">CRAM</option>
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	230 <option value="paf">paf</option>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	231 </param>
15 6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	232 <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" label="don't output base quality"/>
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	233 <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"/>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	234 <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	235 <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.">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	236 <option value="none">no</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	237 <option value="short">short</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	238 <option value="long">long</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	239 </param>
15 6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	240 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Generate CIGAR"
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	241 help="In PAF, the CIGAR is written to the ‘cg’ custom tag." />
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	242
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	243 <param argument="--eqx" type="boolean" truevalue="--eqx" falsevalue="" label="write =/X CIGAR operators"/>
10 8cc404188fae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 1672eb3642d19c8502322115b86846297cd5a6b0 iuc parents: 9 diff changeset	244 <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	245 </section>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	246 </inputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	247 <outputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	248 <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	249 <actions>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	250 <conditional name="reference_source.reference_source_selector">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	251 <when value="cached">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	252 <action type="metadata" name="dbkey">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	253 <option type="from_data_table" name="all_fasta" column="1" offset="0">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	254 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	255 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	256 </option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	257 </action>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	258 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	259 <when value="history">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	260 <action type="metadata" name="dbkey">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	261 <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	262 </action>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	263 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	264 </conditional>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	265 </actions>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	266 <change_format>
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	267 <when input="io_options.output_format" value="paf" format="tabular" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	268 <when input="io_options.output_format" value="CRAM" format="cram" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	269 </change_format>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	270 </data>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	271 </outputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	272 <tests>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	273 <test>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	274 <!-- test single input -->
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	275 <param name="reference_source_selector" value="history" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	276 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	277 <param name="fastq_input_selector" value="single"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	278 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	279 <param name="analysis_type_selector" value="sr"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	280 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	281 </test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	282 <test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	283 <!-- test cram output -->
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	284 <param name="reference_source_selector" value="history" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	285 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	286 <param name="fastq_input_selector" value="single"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	287 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	288 <param name="analysis_type_selector" value="sr"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	289 <param name="output_format" value="CRAM"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	290 <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	291 </test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	292 <test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	293 <!-- test paired input -->
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	294 <param name="reference_source_selector" value="history" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	295 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	296 <param name="fastq_input_selector" value="paired"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	297 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	298 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	299 <param name="analysis_type_selector" value="sr"/>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	300 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	301 </test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	302 <test>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	303 <!-- test paired input with one pair compressed -->
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	304 <param name="reference_source_selector" value="history" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	305 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	306 <param name="fastq_input_selector" value="paired"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	307 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	308 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	309 <param name="analysis_type_selector" value="sr"/>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	310 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	311 </test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	312 <test>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	313 <!-- test collection input -->
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	314 <param name="reference_source_selector" value="history" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	315 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	316 <param name="fastq_input_selector" value="paired_collection"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	317 <param name="fastq_input1">
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	318 <collection type="paired">
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	319 <element name="forward" value="bwa-mem-fastq1.fq" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	320 <element name="reverse" value="bwa-mem-fastq2.fq" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	321 </collection>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	322 </param>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	323 <param name="analysis_type_selector" value="sr"/>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	324 <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="2" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	325 </test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	326 <test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	327 <!-- test data table reference -->
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	328 <param name="reference_source_selector" value="cached" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	329 <param name="ref_file" value="bwa-mem-mt-genome"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	330 <param name="fastq_input_selector" value="single"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	331 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	332 <param name="analysis_type_selector" value="sr"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	333 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	334 </test>
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	335 <test>
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	336 <!-- test paf output -->
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	337 <param name="reference_source_selector" value="history" />
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	338 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" />
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	339 <param name="fastq_input_selector" value="single"/>
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	340 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" />
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	341 <param name="analysis_type_selector" value="ava-ont"/>
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	342 <param name="output_format" value="paf"/>
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	343 <output name="alignment_output" ftype="tabular" file="mini_reads.paf" />
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	344 </test>
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	345 <test>
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	346 <!-- test self-homology mode -->
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	347 <param name="reference_source_selector" value="history" />
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	348 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	349 <param name="fastq_input_selector" value="single" />
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	350 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	351 <param name="analysis_type_selector" value="self-homology" />
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	352 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="2" />
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	353 </test>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	354 </tests>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	355 <help>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	356
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	357 Users’ Guide
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	358 ------------
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	359
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	360 Minimap2 is a versatile sequence alignment program that aligns DNA or
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	361 mRNA sequences against a large reference database. Typical use cases
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	362 include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	363 human genome; (2) finding overlaps between long reads with error rate up
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	364 to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	365 or Direct RNA reads against a reference genome; (4) aligning Illumina
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	366 single- or paired-end reads; (5) assembly-to-assembly alignment; (6)
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	367 full-genome alignment between two closely related species with
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	368 divergence below ~15%.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	369
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	370 For ~10kb noisy reads sequences, minimap2 is tens of times faster than
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	371 mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	372 is more accurate on simulated long reads and produces biologically
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	373 meaningful alignment ready for downstream analyses. For >100bp Illumina
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	374 short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	375 as accurate on simulated data. Detailed evaluations are available from
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	376 the `minimap2 preprint`.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	377
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	378 General usage
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	379 ~~~~~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	380
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	381 Minimap2 seamlessly works with gzip’d FASTA and FASTQ formats as input.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	382 You don’t need to convert between FASTA and FASTQ or decompress gzip’d
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	383 files first.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	384
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	385 For the human reference genome, minimap2 takes a few minutes to generate
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	386 a minimizer index for the reference before mapping. To reduce indexing
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	387 time, you can optionally save the index with option -d and replace
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	388 the reference sequence file with the index file on the minimap2 command
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	389 line:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	390
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	391 *Importantly*, it should be noted that once you build the index,
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	392 indexing parameters such as -k, -w, -H and -I can’t be
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	393 changed during mapping. If you are running minimap2 for different data
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	394 types, you will probably need to keep multiple indexes generated with
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	395 different parameters. This makes minimap2 different from BWA which
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	396 always uses the same index regardless of query data types.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	397
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	398 Use cases
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	399 ~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	400
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	401 Minimap2 uses the same base algorithm for all applications. However, due
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	402 to the different data types it supports (e.g. short vs long reads; DNA
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	403 vs mRNA reads), minimap2 needs to be tuned for optimal performance and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	404 accuracy. It is usually recommended to choose a preset with option
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	405 -x, which sets multiple parameters at the same time. The default
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	406 setting is the same as ``map-ont``.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	407
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	408 Map long noisy genomic reads
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	409 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	410
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	411 The difference between ``map-pb`` and ``map-ont`` is that ``map-pb``
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	412 uses homopolymer-compressed (HPC) minimizers as seeds, while ``map-ont``
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	413 uses ordinary minimizers as seeds. Emperical evaluation suggests HPC
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	414 minimizers improve performance and sensitivity when aligning PacBio
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	415 reads, but hurt when aligning Nanopore reads.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	416
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	417 Map long mRNA/cDNA reads
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	418 ^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	419
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	420
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	421 There are different long-read RNA-seq technologies, including
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	422 tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	423 and Direct RNA-seq. They produce data of varying quality and properties.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	424 By default, ``-x splice`` assumes the read orientation relative to the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	425 transcript strand is unknown. It tries two rounds of alignment to infer
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	426 the orientation and write the strand to the ``ts`` SAM/PAF tag if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	427 possible. For Iso-seq, Direct RNA-seq and tranditional full-length
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	428 cDNAs, it would be desired to apply ``-u f`` to force minimap2 to
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	429 consider the forward transcript strand only. This speeds up alignment
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	430 with slight improvement to accuracy. For noisy Nanopore Direct RNA-seq
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	431 reads, it is recommended to use a smaller k-mer size for increased
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	432 sensitivity to the first or the last exons.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	433
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	434 It is worth noting that by default ``-x splice`` prefers
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	435 GT[A/G]..[C/T]AG over GT[C/T]..[A/G]AG, and then over other splicing
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	436 signals. Considering one additional base improves the junction accuracy
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	437 for noisy reads, but reduces the accuracy when aligning against the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	438 widely used SIRV control data. This is because SIRV does not honor the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	439 evolutionarily conservative splicing signal. If you are studying SIRV,
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	440 you may apply ``--splice-flank=no`` to let minimap2 only model GT..AG,
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	441 ignoring the additional base.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	442
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	443 Find overlaps between long reads
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	444 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	445
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	446 Similarly, ``ava-pb`` uses HPC minimizers while ``ava-ont`` uses
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	447 ordinary minimizers. It is usually not recommended to perform base-level
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	448 alignment in the overlapping mode because it is slow and may produce
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	449 false positive overlaps. However, if performance is not a concern, you
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	450 may try to add ``-a`` or ``-c`` anyway.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	451
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	452 Map short accurate genomic reads
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	453 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	454
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	455
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	456 When two read files are specified, minimap2 reads from each file in turn
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	457 and merge them into an interleaved stream internally. Two reads are
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	458 considered to be paired if they are adjacent in the input stream and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	459 have the same name (with the ``/[0-9]`` suffix trimmed if present).
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	460 Single- and paired-end reads can be mixed.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	461
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	462 Minimap2 does not work well with short spliced reads. There are many
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	463 capable RNA-seq mappers for short reads.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	464
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	465 Full genome/assembly alignment
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	466 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	467
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	468 For cross-species full-genome alignment, the scoring system needs to be
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	469 tuned according to the sequence divergence.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	470
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	471 Self-homology map creation
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	472 ^^^^^^^^^^^^^^^^^^^^^^^^^^
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	473
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	474 A self-homology map is created by mapping a genome (e.g. that of E. coli)
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	475 against itself. When this option is used the same FASTA file should
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	476 be used for reference and for the (single ended mode) query.
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	477
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	478 Advanced features
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	479 ~~~~~~~~~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	480
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	481 Working with >65535 CIGAR operations
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	482 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	483
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	484 Due to a design flaw, BAM does not work with CIGAR strings with >65535
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	485 operations (SAM and CRAM work). However, for ultra-long nanopore reads
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	486 minimap2 may align ~1% of read bases with long CIGARs beyond the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	487 capability of BAM. If you convert such SAM/CRAM to BAM, Picard and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	488 recent samtools will throw an error and abort. Older samtools and other
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	489 tools may create corrupted BAM.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	490
8 6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	491 To avoid this issue, you can add option ``-L`` at the minimap2 command line.
6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	492 This option moves a long CIGAR to the ``CG`` tag and leaves a fully clipped
6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	493 CIGAR at the SAM CIGAR column. Current tools that don’t read CIGAR
6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	494 (e.g. merging and sorting) still work with such BAM records; tools that read
6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	495 CIGAR will effectively ignore these records. It has been decided that future
6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	496 tools will seamlessly recognize long-cigar records generated by option `-L`.
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	497
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	498 TD;DR: if you work with ultra-long reads and use tools that only
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	499 process BAM files, please add option ``-L``.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	500
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	501 The cs optional tag
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	502 ^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	503
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	504 The ``cs`` SAM/PAF tag encodes bases at mismatches and INDELs. It
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	505 matches regular expression
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	506 ``/(:[0-9]+\|\*[a-z][a-z]\|[=\+\-][A-Za-z]+)+/``. Like CIGAR, ``cs``
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	507 consists of series of operations. Each leading character specifies the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	508 operation; the following sequence is the one involved in the operation.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	509
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	510 The ``cs`` tag is enabled by command line option ``--cs``. The following
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	511 alignment, for example:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	512
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	513 .. code::
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	514
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	515 CGATCGATAAATAGAGTAG---GAATAGCA
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	516 \|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	517 CGATCG---AATAGAGTAGGTCGAATtGCA
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	518
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	519 is represented as ``:6-ata:10+gtc:4*at:3``, where ``:[0-9]+`` represents
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	520 an identical block, ``-ata`` represents a deltion, ``+gtc`` an insertion
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	521 and ``*at`` indicates reference base ``a`` is substituted with a query
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	522 base ``t``. It is similar to the ``MD`` SAM tag but is standalone and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	523 easier to parse.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	524
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	525 If ``--cs=long`` is used, the ``cs`` string also contains identical
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	526 sequences in the alignment. The above example will become
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	527 ``=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA``. The long form of ``cs``
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	528 encodes both reference and query sequences in one string.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	529
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	530 Algorithm overview
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	531 ~~~~~~~~~~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	532
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	533 In the following, minimap2 command line options have a dash ahead and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	534 are highlighted in bold. The description may help to tune minimap2
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	535 parameters.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	536
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	537 1. Read -I [=4G] reference bases, extract
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	538 (-k,\ -w)-minimizers and index them in a hash table.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	539
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	540 2. Read -K [=200M] query bases. For each query sequence, do step 3
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	541 through 7:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	542
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	543 3. For each (-k,\ -w)-minimizer on the query, check against the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	544 reference index. If a reference minimizer is not among the top -f
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	545 [=2e-4] most frequent, collect its the occurrences in the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	546 reference, which are called seeds.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	547
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	548 4. Sort seeds by position in the reference. Chain them with dynamic
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	549 programming. Each chain represents a potential mapping. For read
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	550 overlapping, report all chains and then go to step 8. For reference
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	551 mapping, do step 5 through 7:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	552
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	553 5. Let P be the set of primary mappings, which is an empty set
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	554 initially. For each chain from the best to the worst according to
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	555 their chaining scores: if on the query, the chain overlaps with a
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	556 chain in P by –mask-level [=0.5] or higher fraction of the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	557 shorter chain, mark the chain as secondary to the chain in P;
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	558 otherwise, add the chain to P.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	559
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	560 6. Retain all primary mappings. Also retain up to -N [=5] top
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	561 secondary mappings if their chaining scores are higher than -p
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	562 [=0.8] of their corresponding primary mappings.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	563
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	564 7. If alignment is requested, filter out an internal seed if it
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	565 potentially leads to both a long insertion and a long deletion.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	566 Extend from the left-most seed. Perform global alignments between
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	567 internal seeds. Split the chain if the accumulative score along the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	568 global alignment drops by -z [=400], disregarding long gaps.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	569 Extend from the right-most seed. Output chains and their alignments.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	570
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	571 8. If there are more query sequences in the input, go to step 2 until no
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	572 more queries are left.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	573
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	574 9. If there are more reference sequences, reopen the query file from the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	575 start and go to step 1; otherwise stop.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	576
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	577 Limitations
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	578 -----------
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	579
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	580 - Minimap2 may produce suboptimal alignments through long
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	581 low-complexity regions where seed positions may be suboptimal. This
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	582 should not be a big concern because even the optimal alignment may be
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	583 wrong in such regions.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	584 </help>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	585 <citations>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	586 <citation type="doi">10.1093/bioinformatics/btp324</citation>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	587 <citation type="doi">10.1093/bioinformatics/btp698</citation>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	588 <citation type="bibtex">@misc{1303.3997,
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	589 Author = {Heng Li},
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	590 Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	591 Year = {2017},
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	592 Eprint = {arXiv:1708.01492},
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	593 url = {https://arxiv.org/abs/1708.01492},
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	594 }</citation>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	595 </citations>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	596 </tool>

Mercurial > repos > iuc > minimap2

annotate minimap2.xml @ 15:6d5a7cc63314 draft