minimap2: minimap2.xml annotate

annotate minimap2.xml @ 10:77b2770508f6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89"

author	iuc
date	Thu, 11 Feb 2021 19:10:41 +0000
parents	8c6cd2650d1f
children	f54f5baedfdd

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"?>
10 77b2770508f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89" iuc parents: 9 diff changeset	2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy3" 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>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	6 <xml name="pe_anaylsis_fixed_selector">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	7 <param name="analysis_type_selector" type="select"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	8 label="Presets for PE reads alignment"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	9 help="These are the minimap2 preset options for PE alignment of short reads. You can customize these and other settings in the indexing, mapping and alignment options sections below.">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	10 <option value="sr">Short reads without splicing (-k21 -w11 --sr -F800 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	11 </param>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	12 </xml>
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	13 </macros>
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	14 <requirements>
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	15 <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	16 <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	17 </requirements>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	18 <stdio>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	19 <exit_code range="1:" level="fatal" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	20 <regex match="\[ERROR\]" source="stderr" level="fatal" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	21 </stdio>
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	22 <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	23 <command>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	24 <![CDATA[
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	25 #if $reference_source.reference_source_selector == 'history':
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	26 ln -f -s '$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	27 #else:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	28 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	29 #end if
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	30 minimap2
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	31 #if str($fastq_input.analysis_type_selector) == 'self-homology':
7 b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	32 -DP -k19 -w19 -m200
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	33 #elif $fastq_input.analysis_type_selector:
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	34 -x ${fastq_input.analysis_type_selector}
7 b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	35 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	36
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	37 ## 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	38 $indexing_options.H
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	39 #if str($indexing_options.k):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	40 -k $indexing_options.k
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	41 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	42 #if str($indexing_options.w):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	43 -w $indexing_options.w
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	44 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	45 #if str($indexing_options.I):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	46 -I $indexing_options.I
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	47 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	48
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	49 ## Mapping options
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	50 #if str($mapping_options.f):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	51 -f $mapping_options.f
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	52 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	53 #if str($mapping_options.min_occ_floor):
10 77b2770508f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89" iuc parents: 9 diff changeset	54 --min-occ-floor $mapping_options.min_occ_floor
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	55 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	56 #if str($mapping_options.g):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	57 -g $mapping_options.g
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	58 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	59 #if str($mapping_options.r):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	60 -r $mapping_options.r
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	61 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	62 #if str($mapping_options.n):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	63 -n $mapping_options.n
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	64 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	65 #if str($mapping_options.m):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	66 -m $mapping_options.m
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	67 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	68 #if str($mapping_options.max_chain_skip):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	69 --max-chain-skip $mapping_options.max_chain_skip
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	70 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	71 #if str($mapping_options.max_chain_iter):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	72 --max-chain-iter $mapping_options.max_chain_iter
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	73 #end if
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	74 $mapping_options.X
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	75 #if str($mapping_options.p):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	76 -p $mapping_options.p
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	77 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	78 #if str($mapping_options.N):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	79 -N $mapping_options.N
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	80 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	81
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	82 ## Alignment options
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	83 #if str($alignment_options.splicing.splice_mode) == '--splice':
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	84 --frag=no --splice
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	85 #if str($alignment_options.splicing.G):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	86 -G $alignment_options.splicing.G
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	87 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	88 #if str($alignment_options.splicing.C):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	89 -C $alignment_options.splicing.C
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	90 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	91 #if $alignment_options.splicing.u:
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	92 -u $alignment_options.splicing.u
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	93 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	94 $alignment_options.splicing.splice_flank
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	95 #if str($alignment_options.splicing.splice_site_annotations.use_annotations) == 'yes':
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	96 --junc-bed '$alignment_options.splicing.splice_site_annotations.junc_bed'
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	97 --junc-bonus $alignment_options.splicing.splice_site_annotations.junc_bonus
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	98 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	99 #elif str($mapping_options.F) and 'splice' not in str($fastq_input.analysis_type_selector):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	100 --frag=yes -F $mapping_options.F
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	101 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	102 #if str($alignment_options.A):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	103 -A $alignment_options.A
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	104 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	105 #if str($alignment_options.B):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	106 -B $alignment_options.B
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	107 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	108 #if str($alignment_options.O):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	109 #if str($alignment_options.O2):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	110 -O $alignment_options.O,$alignment_options.O2
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	111 #else
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	112 -O $alignment_options.O
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	113 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	114 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	115 #if str($alignment_options.E):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	116 #if str($alignment_options.E2):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	117 -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	118 #else
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	119 -E $alignment_options.E
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	120 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	121 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	122 #if str($alignment_options.z):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	123 #if str($alignment_options.z2):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	124 -z $alignment_options.z,$alignment_options.z2
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	125 #else
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	126 -z $alignment_options.z
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	127 #end if
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	128 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	129 #if str($alignment_options.s):
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	130 -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	131 #end if
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	132 $alignment_options.no_end_flt
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	133 ## Output options
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	134 $io_options.Q
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	135 $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	136 $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	137 #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	138 --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	139 #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	140 $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	141 #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	142 -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	143 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	144 -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	145 reference.fa
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	146 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	147 '$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	148 #else if $fastq_input.fastq_input_selector == 'paired':
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	149 '$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	150 #else if $fastq_input.fastq_input_selector == 'paired_collection':
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	151 '$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	152 #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	153 #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	154 -a
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	155 \| samtools sort
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	156 -@\${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	157 -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	158 -O $io_options.output_format
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	159 -o '$alignment_output'
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	160 #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	161 -a
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	162 \| 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	163 -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	164 -@\${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	165 -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	166 $io_options.eqx
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	167 --reference reference.fa
2 4070f129540a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 79e4c4d7182a4d3f7b6d9a7e444a2bb34be588c0 iuc parents: 1 diff changeset	168 --output-fmt-option no_ref
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	169 -o '$alignment_output'
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	170 #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	171 > '$alignment_output'
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	172 ]]>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	173 </command>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	174 <inputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	175 <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	176 <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	177 <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	178 <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	179 </param>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	180 <when value="cached">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	181 <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	182 <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	183 <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	184 <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	185 </options>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	186 <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	187 </param>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	188 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	189 <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	190 <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	191 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	192 </conditional>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	193 <!-- 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	194 <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	195 <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	196 <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	197 <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	198 <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	199 <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	200 </param>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	201 <!-- below, preset options are only offered for single-end input
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	202 because paired-end alignment in minimap2 is only enabled with -x sr
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	203 (see https://github.com/lh3/minimap2/issues/190) -->
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	204 <when value="single">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	205 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	206 <param name="analysis_type_selector" type="select" optional="True"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	207 label="Select a profile of preset options"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	208 help="Each profile comes with the preconfigured settings mentioned in parentheses. You can customize each profile further in the indexing, mapping and alignment options sections below. If you do not select a profile here, the tool will use the per-parameter defaults listed in the below sections unless you customize them." >
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	209 <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19) (map-pb)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	210 <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>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	211 <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25) (ava-pb)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	212 <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>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	213 <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>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	214 <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>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	215 <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>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	216 <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>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	217 <option value="splice:hq">Long-read splice alignment for PacBio CCS reads (same as `splice` but with -C5 -O6,24 -B4) (splice:hq)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	218 <option value="sr">Short single-end reads without splicing (-k21 -w11 --sr -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	219 <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200) (self-homology)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	220 </param>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	221 </when>
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	222 <when value="paired">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	223 <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	224 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	225 <expand macro="pe_anaylsis_fixed_selector" />
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	226 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	227 <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	228 <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"/>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	229 <expand macro="pe_anaylsis_fixed_selector" />
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	230 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	231 <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	232 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	233 <expand macro="pe_anaylsis_fixed_selector" />
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	234 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	235 </conditional>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	236 <section name="indexing_options" title="Indexing options">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	237 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	238 <param argument="-k" type="integer" min="4" max="28" optional="true" label="k-mer size" help=""/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	239 <param argument="-w" type="integer" min="1" optional="true" label="minimizer window size" help=""/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	240 <param argument="-I" type="integer" min="1" optional="true" label="split index for every N input gigabases" help=""/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	241 </section>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	242 <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	243 <param argument="-N" type="integer" min="0" optional="true" label="retain at most INT secondary alignments" help="default=5"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	244 <param argument="-F" type="integer" min="0" value="" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	245 label="Max fragment length for PE alignment"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	246 help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" />
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	247 <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	248 <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	249 <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	250 <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	251 <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	252 <param argument="-m" type="integer" value="" optional="true" label="minimal chaining score (matching bases minus log gap penalty)" help="default=40"/>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	253 <param argument="--max-chain-skip" type="integer" value="" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	254 label="Maximum seed skips during chaining"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	255 help="A heuristics that stops chaining early. Minimap2 uses dynamic programming for chaining. The time complexity is quadratic in the number of seeds. This option makes minimap2 exit the inner loop if it repeatedly sees seeds already on chains. Set to a large number to switch off this heurstics effectively. default=25" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	256 <param argument="--max-chain-iter" type="integer" value="" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	257 label="Maximum number of partial chains checked during chaining"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	258 help="A heuristics to avoid quadratic time complexity in the worst case. default=5000" />
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	259 <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	260 <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	261 </section>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	262 <section name="alignment_options" title="Alignment options" help="Sets -A, -B, -O, -E, -z, -s, and spliced alignments options." expanded="False">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	263 <conditional name="splicing">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	264 <param name="splice_mode" type="select"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	265 label="Customize spliced alignment mode?"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	266 help="Warning: Minimap2 cannot currently perform spliced alignments of read pairs. If you enable spliced alignment for paired-end data it will be treated as single-end!" >
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	267 <option value="preset">No, use profile setting or leave turned off</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	268 <option value="">Disable spliced alignments (overwrite profile setting if necessary)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	269 <option value="--splice">Yes, enable spliced alignments (--splice)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	270 </param>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	271 <when value="preset" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	272 <when value="" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	273 <when value="--splice">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	274 <param argument="-G" type="integer" value="" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	275 label="Maximum allowed gap on the reference"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	276 help="Higher values cause slower spliced alignment. When in use, this option causes -r (in mapping options) to be set to the same value. default=200k" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	277 <param argument="-C" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	278 label="Cost of non-canonical (non-GT-AG) splicing"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	279 help="default=0" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	280 <param argument="-u" type="select" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	281 label="how to find GT-AG"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	282 help="default=n (don't match GT-AG)">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	283 <option value="n">don't match GT-AG (-un)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	284 <option value="f">transcript strand (-uf)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	285 <option value="b">both strands (-ub)</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	286 </param>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	287 <param argument="--splice-flank" type="boolean" truevalue="--splice-flank=yes" falsevalue="--splice-flank=no" checked="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	288 label="Assume conserved flanking region of splice sites?"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	289 help="Assume the next base to a GT donor site tends to be A/G (91% in human and 92% in mouse) and the preceding base to a AG acceptor tends to be C/T. This trend is evolutionarily conserved, all the way to S. cerevisiae (PMID:18688272). Specifying this option generally leads to higher junction accuracy by several percents, so it is applied by default with --splice. However, the SIRV control does not honor this trend (only ~60%) so this option reduces accuracy. If you are benchmarking minimap2 on SIRV data, please disable this option." />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	290 <conditional name="splice_site_annotations">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	291 <param name="use_annotations" type="select"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	292 label="Use previously annotated splice sites to guide the alignment?"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	293 help="">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	294 <option value="no">No, perform unbiased alignment</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	295 <option value="yes">Yes, favor annotated splice sites</option>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	296 </param>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	297 <when value="no" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	298 <when value="yes">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	299 <param argument="--junc-bed" type="data" format="bed"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	300 label="Dataset with annotated genes or introns"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	301 help="Gene annotations should be provided in BED12 (aka 12-column BED), intron positions in 5-column BED format." />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	302 <param argument="--junc-bonus" type="integer" min="1" value="1"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	303 label="Annotated splice site bonus"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	304 help="Score bonus for a splice donor or acceptor found in annotation." />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	305 </when>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	306 </conditional>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	307 </when>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	308 </conditional>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	309 <param argument="-A" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	310 label="Score for a sequence match" help="default=2"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	311 <param argument="-B" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	312 label="Penalty for a mismatch" help="-B; default=4" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	313 <param argument="-O" type="integer" min="1" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	314 label="Gap open penalties for deletions" help="-O; default=4"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	315 <param name="O2" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	316 label="Gap open penalties for insertions" help="-O; default=24"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	317 <param argument="-E" type="integer" min="1" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	318 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"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	319 help="-E; default=2"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	320 <param name="E2" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	321 label="Gap extension penalty for extending an insertion; if left empty uses the value specified for Gap extension penalties above"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	322 help="-E; default=1"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	323 <param argument="-z" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	324 label="Z-drop threshold for truncating an alignment"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	325 help="Increase to improve the contiguity of alignments at the cost of poorer alignments in the middle. default=400" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	326 <param name="z2" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	327 label="Z-drop threshold for reverse-complementing the query"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	328 help="Decrease to find small inversions at the cost of performance and false positives. default=200" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	329 <param argument="-s" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	330 label="minimal peak DP alignment score" help="default=80"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	331 <param name="no_end_flt" type="boolean" falsevalue="--no-end-flt" truevalue="" checked="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	332 label="Filter seeds towards the ends of chains before performing base-level alignment?" />
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	333 </section>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	334 <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	335 <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	336 <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	337 <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	338 <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	339 </param>
8 53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 diff changeset	340 <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	341 <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	342 <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	343 <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	344 <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	345 <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	346 <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	347 </param>
8 53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 7 diff changeset	348 <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	349 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	350
5 17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 4 diff changeset	351 <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	352 <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	353 </section>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	354 </inputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	355 <outputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	356 <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	357 <actions>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	358 <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	359 <when value="cached">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	360 <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	361 <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	362 <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	363 <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	364 </option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	365 </action>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	366 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	367 <when value="history">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	368 <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	369 <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	370 </action>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	371 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	372 </conditional>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	373 </actions>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	374 <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	375 <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	376 <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	377 </change_format>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	378 </data>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	379 </outputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	380 <tests>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	381 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	382 <!-- test single input -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	383 <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	384 <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	385 <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	386 <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	387 <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	388 <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	389 </test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	390 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	391 <!-- test cram output -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	392 <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	393 <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	394 <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	395 <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	396 <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	397 <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	398 <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	399 </test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	400 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	401 <!-- test paired input -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	402 <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	403 <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	404 <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	405 <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	406 <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	407 <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	408 </test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	409 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	410 <!-- 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	411 <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	412 <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	413 <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	414 <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	415 <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	416 <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	417 </test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	418 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	419 <!-- test collection input -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	420 <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	421 <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	422 <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	423 <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	424 <collection type="paired">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	425 <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	426 <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	427 </collection>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	428 </param>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	429 <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	430 </test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	431 <test>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	432 <!-- 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	433 <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	434 <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	435 <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	436 <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	437 <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	438 <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	439 </test>
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	440 <test>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	441 <!-- test alignment options -->
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	442 <param name="reference_source_selector" value="cached" />
10 77b2770508f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89" iuc parents: 9 diff changeset	443 <param name="min_occ_floor" value="1000"/>
9 8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	444 <param name="ref_file" value="bwa-mem-mt-genome"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	445 <param name="fastq_input_selector" value="single"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	446 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	447 <param name="analysis_type_selector" value="sr"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	448 <section name="alignment_options">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	449 <!-- the folowing settings correspond to the defaults for "sr"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	450 mode. The purpose is to check that all alignment params get
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	451 parsed correctly. -->
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	452 <param name="A" value="2" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	453 <param name="B" value="8" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	454 <param name="O" value="12" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	455 <param name="O2" value="32" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	456 <param name="E" value="2" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	457 <param name="E2" value="1" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	458 <param name="z" value="400" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	459 <param name="s" value="40" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	460 </section>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	461 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	462 </test>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 8 diff changeset	463 <test>
4 6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 3 diff changeset	464 <!-- 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	465 <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	466 <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	467 <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	468 <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	469 <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	470 <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	471 <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	472 </test>
7 b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	473 <test>
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	474 <!-- 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	475 <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	476 <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	477 <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	478 <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	479 <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	480 <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	481 </test>
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	482 </tests>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	483 <help>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	484
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	485 Users’ Guide
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	486 ------------
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	487
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	488 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	489 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	490 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	491 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	492 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	493 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	494 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	495 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	496 divergence below ~15%.
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 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	499 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	500 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	501 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	502 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	503 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	504 the `minimap2 preprint`.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	505
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	506 General usage
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	507 ~~~~~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	508
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	509 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	510 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	511 files first.
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 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	514 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	515 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	516 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	517 line:
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 *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	520 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	521 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	522 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	523 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	524 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	525
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	526 Use cases
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	527 ~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	528
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	529 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	530 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	531 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	532 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	533 -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	534 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	535
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	536 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	537 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	538
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	539 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	540 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	541 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	542 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	543 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	544
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	545 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	546 ^^^^^^^^^^^^^^^^^^^^^^^^
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
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	549 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	550 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	551 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	552 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	553 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	554 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	555 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	556 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	557 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	558 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	559 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	560 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	561
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	562 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	563 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	564 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	565 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	566 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	567 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	568 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	569 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	570
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	571 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	572 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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 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	575 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	576 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	577 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	578 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	579
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	580 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	581 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	582
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	583
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	584 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	585 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	586 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	587 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	588 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	589
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	590 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	591 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	592
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	593 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	594 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	595
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	596 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	597 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	598
7 b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	599 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	600 ^^^^^^^^^^^^^^^^^^^^^^^^^^
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	601
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 6 diff changeset	602 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	603 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	604 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	605
0 2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	606 Advanced features
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	607 ~~~~~~~~~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	608
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	609 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	610 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	611
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	612 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	613 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	614 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	615 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	616 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	617 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	618
1 b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 0 diff changeset	619 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	620 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	621 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	622 (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	623 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	624 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	625
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	626 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	627 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	628
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	629 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	630 ^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	631
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	632 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	633 matches regular expression
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	634 ``/(:[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	635 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	636 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	637
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	638 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	639 alignment, for example:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	640
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	641 .. code::
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	642
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	643 CGATCGATAAATAGAGTAG---GAATAGCA
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	644 \|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	645 CGATCG---AATAGAGTAGGTCGAATtGCA
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	646
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	647 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	648 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	649 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	650 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	651 easier to parse.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	652
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	653 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	654 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	655 ``=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	656 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	657
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	658 Algorithm overview
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	659 ~~~~~~~~~~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	660
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	661 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	662 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	663 parameters.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	664
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	665 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	666 (-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	667
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	668 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	669 through 7:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	670
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	671 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	672 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	673 [=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	674 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	675
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	676 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	677 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	678 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	679 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	680
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	681 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	682 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	683 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	684 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	685 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	686 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	687
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	688 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	689 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	690 [=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	691
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	692 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	693 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	694 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	695 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	696 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	697 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	698
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	699 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	700 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	701
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	702 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	703 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	704
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	705 Limitations
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	706 -----------
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	707
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	708 - 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	709 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	710 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	711 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	712 </help>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	713 <citations>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	714 <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	715 <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	716 <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	717 Author = {Heng Li},
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	718 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	719 Year = {2017},
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	720 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	721 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	722 }</citation>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	723 </citations>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: diff changeset	724 </tool>

Mercurial > repos > iuc > minimap2

annotate minimap2.xml @ 10:77b2770508f6 draft