minimap2: minimap2.xml annotate

annotate minimap2.xml @ 8:53c0b7a1a0c3 draft

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

author	iuc
date	Tue, 07 Apr 2020 18:39:38 -0400
parents	b3eab4b67562
children	8c6cd2650d1f

rev	line source
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	1 <?xml version="1.0"?>
8 53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 diff changeset	2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy1" profile="17.01">
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	4 <macros>
6 3f4d6399997b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 0eca6ecb53be7fb0050b6671d0efe03d79247229 iuc parents: 5 diff changeset	5 <token name="@TOOL_VERSION@">2.17</token>
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	6 </macros>
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	7 <requirements>
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	8 <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement>
17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	9 <requirement type="package" version="1.9">samtools</requirement>
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	10 </requirements>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	11 <version_command>minimap2 --version</version_command>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	12 <command>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	13 <![CDATA[
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	14 #if $reference_source.reference_source_selector == 'history':
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	15 ln -f -s '$reference_source.ref_file' reference.fa &&
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	16 #else:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	17 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	18 #end if
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	19 minimap2
7 b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	20 #if str($analysis_type_selector) == 'self-homology':
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	21 -DP -k19 -w19 -m200
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	22 #else
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	23 -x $analysis_type_selector
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	24 #end if
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	25 ## indexing options
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	26 $indexing_options.H
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	27 #if $indexing_options.k:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	28 -k $indexing_options.k
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	29 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	30 #if $indexing_options.w:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	31 -w $indexing_options.w
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	32 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	33 #if $indexing_options.I:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	34 -I $indexing_options.I
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	35 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	36 ## Mapping options
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	37 #if $mapping_options.f:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	38 -f $mapping_options.f
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	39 #end if
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	40 #if $mapping_options.min_occ_floor:
17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	41 --min-occ-floor $min_occ_floor
17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	42 #end if
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	43 #if $mapping_options.g:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	44 -g $mapping_options.g
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	45 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	46 #if $mapping_options.G:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	47 -G $mapping_options.G
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	48 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	49 #if $mapping_options.F:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	50 -F $mapping_options.F
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	51 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	52 #if $mapping_options.r:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	53 -r $mapping_options.r
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	54 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	55 #if $mapping_options.n:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	56 -n $mapping_options.n
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	57 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	58 #if $mapping_options.m:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	59 -m $mapping_options.m
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	60 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	61 $mapping_options.X
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	62 #if $mapping_options.p:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	63 -p $mapping_options.p
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	64 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	65 #if $mapping_options.N:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	66 -N $mapping_options.N
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	67 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	68 ## Alignment options
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	69 #if $alignment_options.A:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	70 -A $alignment_options.A
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	71 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	72 #if $alignment_options.B:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	73 -B $alignment_options.B
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	74 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	75 #if $alignment_options.O:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	76 #if $alignment_options.O2:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	77 -O $alignment_options.O,$alignment_options.O2
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	78 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	79 -O $alignment_options.O
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	80 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	81 #if $alignment_options.E:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	82 #if $alignment_options.E2:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	83 -E $alignment_options.E,$alignment_options.E2
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	84 #else
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	85 -E $alignment_options
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	86 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	87 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	88 #if $alignment_options.z:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	89 $alignment_options.z
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	90 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	91 #if $alignment_options.s:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	92 -s $alignment_options.s
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	93 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	94 #if $alignment_options.u:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	95 -u $alignment_options.u
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	96 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	97 ## Output options
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	98 $io_options.Q
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	99 $io_options.L
8 53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 diff changeset	100 $io_options.c
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	101 #if $io_options.cs:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	102 --cs $io_options.cs
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	103 #end if
3 1650a97189be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 1672eb3642d19c8502322115b86846297cd5a6b0 iuc parents: 2 diff changeset	104 $io_options.Y
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	105 #if $io_options.K:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	106 -K $io_options.K
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	107 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	108 -t \${GALAXY_SLOTS:-4}
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	109 reference.fa
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	110 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	111 '$fastq_input.fastq_input1'
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	112 #else if $fastq_input.fastq_input_selector == 'paired':
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	113 '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	114 #else if $fastq_input.fastq_input_selector == 'paired_collection':
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	115 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	116 #end if
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	117 #if $io_options.output_format == 'BAM':
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	118 -a
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	119 \| samtools sort
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	120 -@\${GALAXY_SLOTS:-2}
7 b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	121 -T "\${TMPDIR:-.}"
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	122 -O $io_options.output_format
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	123 -o '$alignment_output'
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	124 #else if $io_options.output_format == 'CRAM':
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	125 -a
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	126 \| samtools sort
7 b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	127 -T "\${TMPDIR:-.}"
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	128 -@\${GALAXY_SLOTS:-2}
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	129 -O $io_options.output_format
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	130 $io_options.eqx
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	131 --reference reference.fa
2 4070f129540a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 79e4c4d7182a4d3f7b6d9a7e444a2bb34be588c0 iuc parents: 1 diff changeset	132 --output-fmt-option no_ref
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	133 -o '$alignment_output'
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	134 #end if
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	135 > '$alignment_output'
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	136 ]]>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	137 </command>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	138 <inputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	139 <conditional name="reference_source">
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 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 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	141 <option value="cached">Use a built-in genome index</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	142 <option value="history">Use a genome from history and build index</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	143 </param>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	144 <when value="cached">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	145 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	146 <options from_data_table="all_fasta">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	147 <filter type="sort_by" column="2" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	148 <validator type="no_options" message="No reference genomes are available" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	149 </options>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	151 </param>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	152 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	153 <when value="history">
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 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 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	155 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	156 </conditional>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	157 <section name="indexing_options" title="Indexing options">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	158 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	159 <param argument="-k" type="integer" min="4" max="28" optional="true" label="k-mer size" help=""/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	160 <param argument="-w" type="integer" min="1" optional="true" label="minimizer window size" help=""/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	161 <param argument="-I" type="integer" min="1" optional="true" label="split index for every N input gigabases" help=""/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	162 </section>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	163 <!-- start unchanged copy from bwa-mem -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	164 <conditional name="fastq_input">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	166 <option value="single">Single</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	167 <option value="paired">Paired</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	168 <option value="paired_collection">Paired Collection</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	169 <option value="paired_iv">Paired Interleaved</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	170 </param>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	171 <when value="paired">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	174 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	175 <when value="single">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	177 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	178 <when value="paired_collection">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	180 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	181 <when value="paired_iv">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	183 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	184 </conditional>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	185 <!-- end unchanged copy from bwa-mem -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	186 <param name="analysis_type_selector" type="select" label="Select analysis mode (sets default)">
8 53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 diff changeset	187 <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19) (map-pb)</option>
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 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>
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 diff changeset	189 <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25) (ava-pb)</option>
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 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>
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 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>
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 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>
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 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>
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 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>
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 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>
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 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 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	197 </param>
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 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 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 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 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	205 <param argument="-n" type="integer" value="" optional="true" label="minimal number of minimizers on a chain" help="default=3"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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)"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	209 <param argument="-N" type="integer" min="0" optional="true" label="retain at most INT secondary alignments" help="default=5"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	210 </section>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 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">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	212 <param argument="-A" type="integer" optional="true" label="Score for a sequence match" help="default=2"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	213 <param argument="-B" type="integer" optional="true" label="Penalty for a mismatch" help="-B; default=4" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	214 <param argument="-O" type="integer" min="0" optional="true" label="Gap open penalties for deletions" help="-O; default=4"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	215 <param name="-O2" type="integer" min="0" optional="true" label="Gap open penalties for insertions" help="-O; default=24"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 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"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	218 <param argument="-z" type="integer" optional="true" label="Z-drop score" help="default=400"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	219 <param argument="-s" type="integer" optional="true" label="minimal peak DP alignment score" help="default=80"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	220 <param argument="-u" type="select" optional="true" label="how to find GT-AG">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	221 <option value="n">don't match GT-AG</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	222 <option value="f">transcript strand</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	223 <option value="b">both strands</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	224 </param>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	225 </section>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	226 <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False">
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	227 <param name="output_format" type="select" label="Select an output format">
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	228 <option value="BAM">BAM</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	229 <option value="CRAM">CRAM</option>
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	230 <option value="paf">paf</option>
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	231 </param>
8 53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 diff changeset	232 <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" label="don't output base quality"/>
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 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 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	234 <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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.">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	236 <option value="none">no</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	237 <option value="short">short</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	238 <option value="long">long</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	239 </param>
8 53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 diff changeset	240 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Generate CIGAR"
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 diff changeset	241 help="In PAF, the CIGAR is written to the ‘cg’ custom tag." />
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 diff changeset	242
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	243 <param argument="--eqx" type="boolean" truevalue="--eqx" falsevalue="" label="write =/X CIGAR operators"/>
3 1650a97189be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 1672eb3642d19c8502322115b86846297cd5a6b0 iuc parents: 2 diff changeset	244 <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/>
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	245 </section>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	246 </inputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	247 <outputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d 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)">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	249 <actions>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	250 <conditional name="reference_source.reference_source_selector">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	251 <when value="cached">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	252 <action type="metadata" name="dbkey">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	253 <option type="from_data_table" name="all_fasta" column="1" offset="0">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	254 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	255 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	256 </option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	257 </action>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	258 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	259 <when value="history">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	260 <action type="metadata" name="dbkey">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	261 <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	262 </action>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	263 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	264 </conditional>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	265 </actions>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	266 <change_format>
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	267 <when input="io_options.output_format" value="paf" format="tabular" />
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	268 <when input="io_options.output_format" value="CRAM" format="cram" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	269 </change_format>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	270 </data>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	271 </outputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	272 <tests>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	273 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	274 <!-- test single input -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	275 <param name="reference_source_selector" value="history" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	276 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	277 <param name="fastq_input_selector" value="single"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	278 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	279 <param name="analysis_type_selector" value="sr"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	280 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	281 </test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	282 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	283 <!-- test cram output -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	284 <param name="reference_source_selector" value="history" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	285 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	286 <param name="fastq_input_selector" value="single"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	287 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	288 <param name="analysis_type_selector" value="sr"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	289 <param name="output_format" value="CRAM"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	290 <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	291 </test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	292 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	293 <!-- test paired input -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	294 <param name="reference_source_selector" value="history" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	295 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	296 <param name="fastq_input_selector" value="paired"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	297 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	298 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	299 <param name="analysis_type_selector" value="sr"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	300 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	301 </test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	302 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	303 <!-- test paired input with one pair compressed -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	304 <param name="reference_source_selector" value="history" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	305 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	306 <param name="fastq_input_selector" value="paired"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	307 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	308 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	309 <param name="analysis_type_selector" value="sr"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	310 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	311 </test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	312 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	313 <!-- test collection input -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	314 <param name="reference_source_selector" value="history" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	315 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	316 <param name="fastq_input_selector" value="paired_collection"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	317 <param name="fastq_input1">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	318 <collection type="paired">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	319 <element name="forward" value="bwa-mem-fastq1.fq" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	320 <element name="reverse" value="bwa-mem-fastq2.fq" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	321 </collection>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	322 </param>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	323 <param name="analysis_type_selector" value="sr"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	324 <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="2" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	325 </test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	326 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	327 <!-- test data table reference -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	328 <param name="reference_source_selector" value="cached" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	329 <param name="ref_file" value="bwa-mem-mt-genome"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	330 <param name="fastq_input_selector" value="single"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	331 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	332 <param name="analysis_type_selector" value="sr"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	333 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	334 </test>
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	335 <test>
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	336 <!-- test paf output -->
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	337 <param name="reference_source_selector" value="history" />
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	338 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" />
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	339 <param name="fastq_input_selector" value="single"/>
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	340 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" />
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	341 <param name="analysis_type_selector" value="ava-ont"/>
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	342 <param name="output_format" value="paf"/>
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	343 <output name="alignment_output" ftype="tabular" file="mini_reads.paf" />
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	344 </test>
7 b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	345 <test>
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	346 <!-- test self-homology mode -->
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	347 <param name="reference_source_selector" value="history" />
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	348 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	349 <param name="fastq_input_selector" value="single" />
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	350 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	351 <param name="analysis_type_selector" value="self-homology" />
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	352 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="2" />
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	353 </test>
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	354 </tests>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	355 <help>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	356
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	357 Users’ Guide
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	358 ------------
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	359
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	360 Minimap2 is a versatile sequence alignment program that aligns DNA or
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	361 mRNA sequences against a large reference database. Typical use cases
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	362 include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	363 human genome; (2) finding overlaps between long reads with error rate up
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	364 to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	365 or Direct RNA reads against a reference genome; (4) aligning Illumina
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	366 single- or paired-end reads; (5) assembly-to-assembly alignment; (6)
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	367 full-genome alignment between two closely related species with
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	368 divergence below ~15%.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	369
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	370 For ~10kb noisy reads sequences, minimap2 is tens of times faster than
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	371 mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	372 is more accurate on simulated long reads and produces biologically
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	373 meaningful alignment ready for downstream analyses. For >100bp Illumina
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	374 short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	375 as accurate on simulated data. Detailed evaluations are available from
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	376 the `minimap2 preprint`.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	377
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	378 General usage
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	379 ~~~~~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	380
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	381 Minimap2 seamlessly works with gzip’d FASTA and FASTQ formats as input.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	382 You don’t need to convert between FASTA and FASTQ or decompress gzip’d
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	383 files first.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	384
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	385 For the human reference genome, minimap2 takes a few minutes to generate
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	386 a minimizer index for the reference before mapping. To reduce indexing
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	387 time, you can optionally save the index with option -d and replace
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	388 the reference sequence file with the index file on the minimap2 command
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	389 line:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	390
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	391 *Importantly*, it should be noted that once you build the index,
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	392 indexing parameters such as -k, -w, -H and -I can’t be
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	393 changed during mapping. If you are running minimap2 for different data
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	394 types, you will probably need to keep multiple indexes generated with
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	395 different parameters. This makes minimap2 different from BWA which
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	396 always uses the same index regardless of query data types.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	397
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	398 Use cases
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	399 ~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	400
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	401 Minimap2 uses the same base algorithm for all applications. However, due
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	402 to the different data types it supports (e.g. short vs long reads; DNA
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	403 vs mRNA reads), minimap2 needs to be tuned for optimal performance and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	404 accuracy. It is usually recommended to choose a preset with option
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	405 -x, which sets multiple parameters at the same time. The default
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	406 setting is the same as ``map-ont``.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	407
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	408 Map long noisy genomic reads
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	409 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	410
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	411 The difference between ``map-pb`` and ``map-ont`` is that ``map-pb``
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	412 uses homopolymer-compressed (HPC) minimizers as seeds, while ``map-ont``
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	413 uses ordinary minimizers as seeds. Emperical evaluation suggests HPC
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	414 minimizers improve performance and sensitivity when aligning PacBio
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	415 reads, but hurt when aligning Nanopore reads.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	416
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	417 Map long mRNA/cDNA reads
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	418 ^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	419
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	420
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	421 There are different long-read RNA-seq technologies, including
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	422 tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	423 and Direct RNA-seq. They produce data of varying quality and properties.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	424 By default, ``-x splice`` assumes the read orientation relative to the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	425 transcript strand is unknown. It tries two rounds of alignment to infer
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	426 the orientation and write the strand to the ``ts`` SAM/PAF tag if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	427 possible. For Iso-seq, Direct RNA-seq and tranditional full-length
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	428 cDNAs, it would be desired to apply ``-u f`` to force minimap2 to
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	429 consider the forward transcript strand only. This speeds up alignment
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	430 with slight improvement to accuracy. For noisy Nanopore Direct RNA-seq
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	431 reads, it is recommended to use a smaller k-mer size for increased
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	432 sensitivity to the first or the last exons.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	433
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	434 It is worth noting that by default ``-x splice`` prefers
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	435 GT[A/G]..[C/T]AG over GT[C/T]..[A/G]AG, and then over other splicing
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	436 signals. Considering one additional base improves the junction accuracy
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	437 for noisy reads, but reduces the accuracy when aligning against the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	438 widely used SIRV control data. This is because SIRV does not honor the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	439 evolutionarily conservative splicing signal. If you are studying SIRV,
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	440 you may apply ``--splice-flank=no`` to let minimap2 only model GT..AG,
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	441 ignoring the additional base.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	442
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	443 Find overlaps between long reads
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	444 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	445
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	446 Similarly, ``ava-pb`` uses HPC minimizers while ``ava-ont`` uses
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	447 ordinary minimizers. It is usually not recommended to perform base-level
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	448 alignment in the overlapping mode because it is slow and may produce
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	449 false positive overlaps. However, if performance is not a concern, you
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	450 may try to add ``-a`` or ``-c`` anyway.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	451
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	452 Map short accurate genomic reads
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	453 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	454
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	455
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	456 When two read files are specified, minimap2 reads from each file in turn
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	457 and merge them into an interleaved stream internally. Two reads are
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	458 considered to be paired if they are adjacent in the input stream and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	459 have the same name (with the ``/[0-9]`` suffix trimmed if present).
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	460 Single- and paired-end reads can be mixed.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	461
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	462 Minimap2 does not work well with short spliced reads. There are many
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	463 capable RNA-seq mappers for short reads.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	464
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	465 Full genome/assembly alignment
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	466 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	467
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	468 For cross-species full-genome alignment, the scoring system needs to be
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	469 tuned according to the sequence divergence.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	470
7 b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	471 Self-homology map creation
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	472 ^^^^^^^^^^^^^^^^^^^^^^^^^^
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	473
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	474 A self-homology map is created by mapping a genome (e.g. that of E. coli)
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	475 against itself. When this option is used the same FASTA file should
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	476 be used for reference and for the (single ended mode) query.
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	477
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	478 Advanced features
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	479 ~~~~~~~~~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	480
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	481 Working with >65535 CIGAR operations
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	482 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	483
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	484 Due to a design flaw, BAM does not work with CIGAR strings with >65535
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	485 operations (SAM and CRAM work). However, for ultra-long nanopore reads
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	486 minimap2 may align ~1% of read bases with long CIGARs beyond the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	487 capability of BAM. If you convert such SAM/CRAM to BAM, Picard and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	488 recent samtools will throw an error and abort. Older samtools and other
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	489 tools may create corrupted BAM.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	490
1 b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 0 diff changeset	491 To avoid this issue, you can add option ``-L`` at the minimap2 command line.
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 0 diff changeset	492 This option moves a long CIGAR to the ``CG`` tag and leaves a fully clipped
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 0 diff changeset	493 CIGAR at the SAM CIGAR column. Current tools that don’t read CIGAR
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 0 diff changeset	494 (e.g. merging and sorting) still work with such BAM records; tools that read
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 0 diff changeset	495 CIGAR will effectively ignore these records. It has been decided that future
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 0 diff changeset	496 tools will seamlessly recognize long-cigar records generated by option `-L`.
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	497
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	498 TD;DR: if you work with ultra-long reads and use tools that only
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	499 process BAM files, please add option ``-L``.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	500
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	501 The cs optional tag
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	502 ^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	503
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	504 The ``cs`` SAM/PAF tag encodes bases at mismatches and INDELs. It
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	505 matches regular expression
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	506 ``/(:[0-9]+\|\*[a-z][a-z]\|[=\+\-][A-Za-z]+)+/``. Like CIGAR, ``cs``
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	507 consists of series of operations. Each leading character specifies the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	508 operation; the following sequence is the one involved in the operation.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	509
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	510 The ``cs`` tag is enabled by command line option ``--cs``. The following
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	511 alignment, for example:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	512
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	513 .. code::
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	514
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	515 CGATCGATAAATAGAGTAG---GAATAGCA
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	516 \|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	517 CGATCG---AATAGAGTAGGTCGAATtGCA
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	518
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	519 is represented as ``:6-ata:10+gtc:4*at:3``, where ``:[0-9]+`` represents
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	520 an identical block, ``-ata`` represents a deltion, ``+gtc`` an insertion
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	521 and ``*at`` indicates reference base ``a`` is substituted with a query
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	522 base ``t``. It is similar to the ``MD`` SAM tag but is standalone and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	523 easier to parse.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	524
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	525 If ``--cs=long`` is used, the ``cs`` string also contains identical
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	526 sequences in the alignment. The above example will become
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	527 ``=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA``. The long form of ``cs``
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	528 encodes both reference and query sequences in one string.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	529
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	530 Algorithm overview
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	531 ~~~~~~~~~~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	532
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	533 In the following, minimap2 command line options have a dash ahead and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	534 are highlighted in bold. The description may help to tune minimap2
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	535 parameters.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	536
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	537 1. Read -I [=4G] reference bases, extract
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	538 (-k,\ -w)-minimizers and index them in a hash table.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	539
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	540 2. Read -K [=200M] query bases. For each query sequence, do step 3
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	541 through 7:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	542
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	543 3. For each (-k,\ -w)-minimizer on the query, check against the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	544 reference index. If a reference minimizer is not among the top -f
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	545 [=2e-4] most frequent, collect its the occurrences in the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	546 reference, which are called seeds.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	547
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	548 4. Sort seeds by position in the reference. Chain them with dynamic
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	549 programming. Each chain represents a potential mapping. For read
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	550 overlapping, report all chains and then go to step 8. For reference
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	551 mapping, do step 5 through 7:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	552
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	553 5. Let P be the set of primary mappings, which is an empty set
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	554 initially. For each chain from the best to the worst according to
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	555 their chaining scores: if on the query, the chain overlaps with a
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	556 chain in P by –mask-level [=0.5] or higher fraction of the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	557 shorter chain, mark the chain as secondary to the chain in P;
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	558 otherwise, add the chain to P.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	559
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	560 6. Retain all primary mappings. Also retain up to -N [=5] top
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	561 secondary mappings if their chaining scores are higher than -p
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	562 [=0.8] of their corresponding primary mappings.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	563
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	564 7. If alignment is requested, filter out an internal seed if it
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	565 potentially leads to both a long insertion and a long deletion.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	566 Extend from the left-most seed. Perform global alignments between
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	567 internal seeds. Split the chain if the accumulative score along the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	568 global alignment drops by -z [=400], disregarding long gaps.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	569 Extend from the right-most seed. Output chains and their alignments.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	570
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	571 8. If there are more query sequences in the input, go to step 2 until no
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	572 more queries are left.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	573
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	574 9. If there are more reference sequences, reopen the query file from the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	575 start and go to step 1; otherwise stop.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	576
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	577 Limitations
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	578 -----------
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	579
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	580 - Minimap2 may produce suboptimal alignments through long
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	581 low-complexity regions where seed positions may be suboptimal. This
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	582 should not be a big concern because even the optimal alignment may be
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	583 wrong in such regions.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	584 </help>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	585 <citations>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	586 <citation type="doi">10.1093/bioinformatics/btp324</citation>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	587 <citation type="doi">10.1093/bioinformatics/btp698</citation>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	588 <citation type="bibtex">@misc{1303.3997,
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	589 Author = {Heng Li},
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	590 Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	591 Year = {2017},
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	592 Eprint = {arXiv:1708.01492},
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	593 url = {https://arxiv.org/abs/1708.01492},
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	594 }</citation>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	595 </citations>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	596 </tool>

Mercurial > repos > iuc > minimap2

annotate minimap2.xml @ 8:53c0b7a1a0c3 draft