minimap2: minimap2.xml annotate

annotate minimap2.xml @ 22:b81d44caa1a0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

author	iuc
date	Wed, 01 Sep 2021 07:39:22 +0000
parents	597f238f2b4d
children	a9c0055e479a

rev	line source
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	1 <?xml version="1.0"?>
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
22 b81d44caa1a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 21 diff changeset	4 <xrefs>
b81d44caa1a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 21 diff changeset	5 <xref type="bio.tools">minimap2</xref>
b81d44caa1a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 21 diff changeset	6 </xrefs>
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	7 <macros>
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	8 <import>macros.xml</import>
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	9 </macros>
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	10 <expand macro="edam_ontology"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	11 <expand macro="requirements"/>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	12 <stdio>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	13 <exit_code range="1:" level="fatal" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	14 <regex match="\[ERROR\]" source="stderr" level="fatal" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	15 </stdio>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	16 <version_command>minimap2 --version</version_command>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	17 <command>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	18 <![CDATA[
5 3875e9b17ca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: 4 diff changeset	19 #if $reference_source.reference_source_selector == 'history':
3 acb6d016cabe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: 0 diff changeset	20 ln -f -s '$reference_source.ref_file' reference.fa &&
acb6d016cabe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: 0 diff changeset	21 #else:
6 4d84d86b368e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: 5 diff changeset	22 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
4 cd71cf88d971 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: 3 diff changeset	23 #end if
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	24 minimap2
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	25 #if str($fastq_input.analysis_type_selector) == 'self-homology':
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	26 -DP -k19 -w19 -m200
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	27 #elif $fastq_input.analysis_type_selector:
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	28 -x ${fastq_input.analysis_type_selector}
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	29 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	30
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	31 ## indexing options
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	32 $indexing_options.H
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	33 #if str($indexing_options.k):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	34 -k $indexing_options.k
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	35 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	36 #if str($indexing_options.w):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	37 -w $indexing_options.w
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	38 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	39 #if str($indexing_options.I):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	40 -I $indexing_options.I
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	41 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	42
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	43 ## Mapping options
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	44 #if str($mapping_options.f):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	45 -f $mapping_options.f
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	46 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	47 #if str($mapping_options.min_occ_floor):
17 f25bf202bc17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89" iuc parents: 16 diff changeset	48 --min-occ-floor $mapping_options.min_occ_floor
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	49 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	50 #if str($mapping_options.g):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	51 -g $mapping_options.g
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	52 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	53 #if str($mapping_options.r):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	54 -r $mapping_options.r
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	55 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	56 #if str($mapping_options.n):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	57 -n $mapping_options.n
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	58 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	59 #if str($mapping_options.m):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	60 -m $mapping_options.m
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	61 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	62 #if str($mapping_options.max_chain_skip):
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	63 --max-chain-skip $mapping_options.max_chain_skip
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	64 #end if
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	65 #if str($mapping_options.max_chain_iter):
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	66 --max-chain-iter $mapping_options.max_chain_iter
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	67 #end if
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	68 $mapping_options.X
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	69 #if str($mapping_options.p):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	70 -p $mapping_options.p
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	71 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	72 #if str($mapping_options.N):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	73 -N $mapping_options.N
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	74 #end if
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	75 #if str($mapping_options.mask_len):
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	76 --mask-len $mapping_options.mask_len
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	77 #end if
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	78 #if str($mapping_options.kmer_ocurrence_interval.interval):
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	79 -U $mapping_options.kmer_ocurrence_interval.lower_limit,$mapping_options.kmer_ocurrence_interval.upper_limit
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	80 #end if
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	81 ## Alignment options
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	82 #if str($alignment_options.splicing.splice_mode) == '--splice':
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	83 --frag=no --splice
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	84 #if str($alignment_options.splicing.G):
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	85 -G $alignment_options.splicing.G
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	86 #end if
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	87 #if str($alignment_options.splicing.C):
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	88 -C $alignment_options.splicing.C
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	89 #end if
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	90 #if $alignment_options.splicing.u:
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	91 -u $alignment_options.splicing.u
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	92 #end if
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	93 $alignment_options.splicing.splice_flank
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	94 #if str($alignment_options.splicing.splice_site_annotations.use_annotations) == 'yes':
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	95 --junc-bed '$alignment_options.splicing.splice_site_annotations.junc_bed'
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	96 --junc-bonus $alignment_options.splicing.splice_site_annotations.junc_bonus
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	97 #end if
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	98 #elif str($mapping_options.F) and 'splice' not in str($fastq_input.analysis_type_selector):
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	99 --frag=yes -F $mapping_options.F
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	100 #end if
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	101 #if str($alignment_options.A):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	102 -A $alignment_options.A
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	103 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	104 #if str($alignment_options.B):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	105 -B $alignment_options.B
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	106 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	107 #if str($alignment_options.O):
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	108 #if str($alignment_options.O2):
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	109 -O $alignment_options.O,$alignment_options.O2
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	110 #else
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	111 -O $alignment_options.O
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	112 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	113 #end if
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	114 #if str($alignment_options.E):
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	115 #if str($alignment_options.E2):
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	116 -E $alignment_options.E,$alignment_options.E2
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	117 #else
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	118 -E $alignment_options.E
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	119 #end if
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	120 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	121 #if str($alignment_options.z):
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	122 #if str($alignment_options.z2):
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	123 -z $alignment_options.z,$alignment_options.z2
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	124 #else
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	125 -z $alignment_options.z
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	126 #end if
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	127 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	128 #if str($alignment_options.s):
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	129 -s $alignment_options.s
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	130 #end if
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	131 $alignment_options.no_end_flt
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	132 ## Output options
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	133 $io_options.Q
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	134 $io_options.L
15 6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	135 $io_options.c
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	136 #if $io_options.cs:
21 597f238f2b4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243" iuc parents: 20 diff changeset	137 --cs=$io_options.cs
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	138 #end if
10 8cc404188fae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 1672eb3642d19c8502322115b86846297cd5a6b0 iuc parents: 9 diff changeset	139 $io_options.Y
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	140 #if $io_options.K:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	141 -K $io_options.K
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	142 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	143 -t \${GALAXY_SLOTS:-4}
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	144 reference.fa
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	145 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	146 '$fastq_input.fastq_input1'
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	147 #else if $fastq_input.fastq_input_selector == 'paired':
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	148 '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	149 #else if $fastq_input.fastq_input_selector == 'paired_collection':
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	150 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	151 #end if
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	152 #if str($io_options.output_format) in ('BAM', 'CRAM'):
bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	153 -a \| samtools view --no-PG -hT reference.fa
bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	154 #end if
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	155 #if $io_options.output_format == 'BAM':
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	156 \| samtools sort
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	157 -@\${GALAXY_SLOTS:-2}
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	158 -T "\${TMPDIR:-.}"
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	159 -O $io_options.output_format
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	160 -o '$alignment_output'
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	161 #else if $io_options.output_format == 'CRAM':
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	162 \| samtools sort
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	163 -T "\${TMPDIR:-.}"
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	164 -@\${GALAXY_SLOTS:-2}
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	165 -O $io_options.output_format
12 440100db1333 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad iuc parents: 11 diff changeset	166 $io_options.eqx
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	167 --reference reference.fa
9 e738fb9d4a22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ba952bea405513c0d81a33019a4c2fbcdcf8e783 iuc parents: 8 diff changeset	168 --output-fmt-option no_ref
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	169 -o '$alignment_output'
18 0969cc2ddf5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 9eebe4bec24764deefcf7005abd588be29f4594f" iuc parents: 17 diff changeset	170 #else:
0969cc2ddf5f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 9eebe4bec24764deefcf7005abd588be29f4594f" iuc parents: 17 diff changeset	171 > '$alignment_output'
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	172 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	173 ]]>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	174 </command>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	175 <inputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	176 <conditional name="reference_source">
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	177 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	178 <option value="cached">Use a built-in genome index</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	179 <option value="history">Use a genome from history and build index</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	180 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	181 <when value="cached">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	182 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	183 <options from_data_table="all_fasta">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	184 <filter type="sort_by" column="2" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	185 <validator type="no_options" message="No reference genomes are available" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	186 </options>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	187 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	188 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	189 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	190 <when value="history">
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	191 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	192 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	193 </conditional>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	194 <!-- start unchanged copy from bwa-mem -->
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	195 <conditional name="fastq_input">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	196 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	197 <option value="single">Single</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	198 <option value="paired">Paired</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	199 <option value="paired_collection">Paired Collection</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	200 <option value="paired_iv">Paired Interleaved</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	201 </param>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	202 <!-- below, preset options are only offered for single-end input
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	203 because paired-end alignment in minimap2 is only enabled with -x sr
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	204 (see https://github.com/lh3/minimap2/issues/190) -->
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	205 <when value="single">
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	206 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	207 <param name="analysis_type_selector" type="select" optional="True"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	208 label="Select a profile of preset options"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	209 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." >
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	210 <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19) (map-pb)</option>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	211 <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>
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	212 <option value="map-hifi">PacBio HiFi reads vs reference mapping (-k19 -w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1 -s200 ) (map-hifi)</option>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	213 <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25) (ava-pb)</option>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	214 <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>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	215 <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>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	216 <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>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	217 <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>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	218 <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>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	219 <option value="splice:hq">Long-read splice alignment for PacBio CCS reads (same as `splice` but with -C5 -O6,24 -B4) (splice:hq)</option>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	220 <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>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	221 <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200) (self-homology)</option>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	222 </param>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	223 </when>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	224 <when value="paired">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	225 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	226 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	227 <expand macro="pe_anaylsis_fixed_selector" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	228 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	229 <when value="paired_collection">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	230 <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"/>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	231 <expand macro="pe_anaylsis_fixed_selector" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	232 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	233 <when value="paired_iv">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	234 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	235 <expand macro="pe_anaylsis_fixed_selector" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	236 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	237 </conditional>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	238 <section name="indexing_options" title="Indexing options">
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	239 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	240 <param argument="-k" type="integer" min="4" max="28" optional="true" label="K-mer size" help=""/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	241 <param argument="-w" type="integer" min="1" optional="true" label="Minimizer window size" help=""/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	242 <param argument="-I" type="integer" min="1" optional="true" label="Split index for every N input gigabases" help=""/>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	243 </section>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	244 <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">
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	245 <param argument="-N" type="integer" min="0" optional="true" label="Retain at most INT secondary alignments" help="default=5"/>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	246 <param argument="-F" type="integer" min="0" value="" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	247 label="Max fragment length for PE alignment"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	248 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" />
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	249 <param argument="-f" type="float" value="" optional="true" label="Filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	250 <conditional name="kmer_ocurrence_interval">
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	251 <param name="interval" argument="-U" type="select" label="Specify an interval of k-mer occurrences" help="Allows to specify an interval of k-mer occurrences with -U. For repeat-rich genomes, the automatic k-mer occurrence threshold determined by -f may be too large and makes alignment impractically slow. The new option protects against such cases. Enabled for asm* and map-hifi.">
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	252 <option value="enabled">Enabled</option>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	253 <option value="" selected="true">Disabled</option>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	254 </param>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	255 <when value="enabled">
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	256 <param name="lower_limit" type="integer" min="0" max="10000" value="" label="K-mer ocurrence lower limit"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	257 <param name="upper_limit" type="integer" min="0" max="10000" value="" label="K-mer ocurrence upper limit"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	258 </when>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	259 <when value="">
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	260 </when>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	261 </conditional>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	262 <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" />
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	263 <param argument="-g" type="integer" value="" optional="true" label="Stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	264 <param argument="-r" type="integer" value="" optional="true" label="Bandwidth used in chaining and DP-based alignment" help="default=500" />
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	265 <param argument="-n" type="integer" value="" optional="true" label="Minimal number of minimizers on a chain" help="default=3"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	266 <param argument="-m" type="integer" value="" optional="true" label="Minimal chaining score (matching bases minus log gap penalty)" help="default=40"/>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	267 <param argument="--max-chain-skip" type="integer" value="" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	268 label="Maximum seed skips during chaining"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	269 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" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	270 <param argument="--max-chain-iter" type="integer" value="" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	271 label="Maximum number of partial chains checked during chaining"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	272 help="A heuristics to avoid quadratic time complexity in the worst case. default=5000" />
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	273 <param argument="-X" type="boolean" truevalue="-X" falsevalue="" optional="true" label="Skip self and dual mappings (for the all-vs-all mode)"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	274 <param argument="-p" type="float" value="" max="1" optional="true" label="Min secondary-to-primary score ratio" help="default=0.8"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	275 <param argument="--mask-len" type="integer" min="0" max="10000" value="" optional="true" label="Fine control the removal of redundant hits" help="Keep an alignment if dropping it leaves an unaligned region on query longer than INT"/>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	276 </section>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	277 <section name="alignment_options" title="Alignment options" help="Sets -A, -B, -O, -E, -z, -s, and spliced alignments options." expanded="False">
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	278 <conditional name="splicing">
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	279 <param name="splice_mode" type="select"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	280 label="Customize spliced alignment mode?"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	281 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!" >
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	282 <option value="preset">No, use profile setting or leave turned off</option>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	283 <option value="">Disable spliced alignments (overwrite profile setting if necessary)</option>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	284 <option value="--splice">Yes, enable spliced alignments (--splice)</option>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	285 </param>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	286 <when value="preset" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	287 <when value="" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	288 <when value="--splice">
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	289 <param argument="-G" type="integer" value="" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	290 label="Maximum allowed gap on the reference"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	291 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" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	292 <param argument="-C" type="integer" min="0" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	293 label="Cost of non-canonical (non-GT-AG) splicing"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	294 help="default=0" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	295 <param argument="-u" type="select" optional="true"
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	296 label="How to find GT-AG"
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	297 help="default=n (don't match GT-AG)">
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	298 <option value="n">Don't match GT-AG (-un)</option>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	299 <option value="f">Transcript strand (-uf)</option>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	300 <option value="b">Both strands (-ub)</option>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	301 </param>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	302 <param argument="--splice-flank" type="boolean" truevalue="--splice-flank=yes" falsevalue="--splice-flank=no" checked="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	303 label="Assume conserved flanking region of splice sites?"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	304 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." />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	305 <conditional name="splice_site_annotations">
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	306 <param name="use_annotations" type="select"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	307 label="Use previously annotated splice sites to guide the alignment?"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	308 help="">
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	309 <option value="no">No, perform unbiased alignment</option>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	310 <option value="yes">Yes, favor annotated splice sites</option>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	311 </param>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	312 <when value="no" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	313 <when value="yes">
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	314 <param argument="--junc-bed" type="data" format="bed"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	315 label="Dataset with annotated genes or introns"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	316 help="Gene annotations should be provided in BED12 (aka 12-column BED), intron positions in 5-column BED format." />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	317 <param argument="--junc-bonus" type="integer" min="1" value="1"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	318 label="Annotated splice site bonus"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	319 help="Score bonus for a splice donor or acceptor found in annotation." />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	320 </when>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	321 </conditional>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	322 </when>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	323 </conditional>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	324 <param argument="-A" type="integer" min="0" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	325 label="Score for a sequence match" help="default=2"/>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	326 <param argument="-B" type="integer" min="0" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	327 label="Penalty for a mismatch" help="-B; default=4" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	328 <param argument="-O" type="integer" min="1" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	329 label="Gap open penalties for deletions" help="-O; default=4"/>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	330 <param name="O2" type="integer" min="0" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	331 label="Gap open penalties for insertions" help="-O; default=24"/>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	332 <param argument="-E" type="integer" min="1" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	333 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"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	334 help="-E; default=2"/>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	335 <param name="E2" type="integer" min="0" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	336 label="Gap extension penalty for extending an insertion; if left empty uses the value specified for Gap extension penalties above"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	337 help="-E; default=1"/>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	338 <param argument="-z" type="integer" min="0" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	339 label="Z-drop threshold for truncating an alignment"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	340 help="Increase to improve the contiguity of alignments at the cost of poorer alignments in the middle. default=400" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	341 <param name="z2" type="integer" min="0" optional="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	342 label="Z-drop threshold for reverse-complementing the query"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	343 help="Decrease to find small inversions at the cost of performance and false positives. default=200" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	344 <param argument="-s" type="integer" min="0" optional="true"
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	345 label="Minimal peak DP alignment score" help="default=80"/>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	346 <param name="no_end_flt" type="boolean" falsevalue="--no-end-flt" truevalue="" checked="true"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	347 label="Filter seeds towards the ends of chains before performing base-level alignment?" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	348 </section>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	349 <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False">
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	350 <param name="output_format" type="select" label="Select an output format">
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	351 <option value="BAM">BAM</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	352 <option value="CRAM">CRAM</option>
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	353 <option value="paf">PAF</option>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	354 </param>
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	355 <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" label="Don't output base quality"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	356 <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"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	357 <param argument="-K" type="integer" optional="true" label="Minibatch size for mapping (in megabyte)" help="default=500M"/>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	358 <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below.">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	359 <option value="none">no</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	360 <option value="short">short</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	361 <option value="long">long</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	362 </param>
15 6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	363 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Generate CIGAR"
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	364 help="In PAF, the CIGAR is written to the ‘cg’ custom tag." />
6d5a7cc63314 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba" iuc parents: 14 diff changeset	365
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	366 <param argument="--eqx" type="boolean" truevalue="--eqx" falsevalue="" label="Write =/X CIGAR operators"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	367 <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments ?"/>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	368 </section>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	369 </inputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	370 <outputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	371 <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	372 <actions>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	373 <conditional name="reference_source.reference_source_selector">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	374 <when value="cached">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	375 <action type="metadata" name="dbkey">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	376 <option type="from_data_table" name="all_fasta" column="1" offset="0">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	377 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	378 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	379 </option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	380 </action>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	381 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	382 <when value="history">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	383 <action type="metadata" name="dbkey">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	384 <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	385 </action>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	386 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	387 </conditional>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	388 </actions>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	389 <change_format>
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	390 <when input="io_options.output_format" value="paf" format="tabular" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	391 <when input="io_options.output_format" value="CRAM" format="cram" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	392 </change_format>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	393 </data>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	394 </outputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	395 <tests>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	396 <test>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	397 <!-- test single input -->
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	398 <param name="reference_source_selector" value="history" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	399 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	400 <param name="fastq_input_selector" value="single"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	401 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	402 <param name="analysis_type_selector" value="sr"/>
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	403 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	404 </test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	405 <test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	406 <!-- test cram output -->
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	407 <param name="reference_source_selector" value="history" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	408 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	409 <param name="fastq_input_selector" value="single"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	410 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	411 <param name="analysis_type_selector" value="sr"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	412 <param name="output_format" value="CRAM"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	413 <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	414 </test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	415 <test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	416 <!-- test paired input -->
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	417 <param name="reference_source_selector" value="history" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	418 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	419 <param name="fastq_input_selector" value="paired"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	420 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	421 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	422 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	423 </test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	424 <test>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	425 <!-- test paired input with one pair compressed -->
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	426 <param name="reference_source_selector" value="history" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	427 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	428 <param name="fastq_input_selector" value="paired"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	429 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	430 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	431 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	432 </test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	433 <test>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	434 <!-- test collection input -->
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	435 <param name="reference_source_selector" value="history" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	436 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	437 <param name="fastq_input_selector" value="paired_collection"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	438 <param name="fastq_input1">
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	439 <collection type="paired">
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	440 <element name="forward" value="bwa-mem-fastq1.fq" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	441 <element name="reverse" value="bwa-mem-fastq2.fq" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	442 </collection>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	443 </param>
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	444 <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" />
7 831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	445 </test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	446 <test>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	447 <!-- test data table reference -->
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	448 <param name="reference_source_selector" value="cached" />
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	449 <param name="ref_file" value="bwa-mem-mt-genome"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	450 <param name="fastq_input_selector" value="single"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	451 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
831dcb48efa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d iuc parents: 6 diff changeset	452 <param name="analysis_type_selector" value="sr"/>
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	453 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	454 </test>
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	455 <test>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	456 <!-- test alignment options -->
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	457 <param name="reference_source_selector" value="cached" />
17 f25bf202bc17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89" iuc parents: 16 diff changeset	458 <param name="min_occ_floor" value="1000"/>
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	459 <param name="ref_file" value="bwa-mem-mt-genome"/>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	460 <param name="fastq_input_selector" value="single"/>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	461 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	462 <param name="analysis_type_selector" value="sr"/>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	463 <section name="alignment_options">
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	464 <!-- the folowing settings correspond to the defaults for "sr"
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	465 mode. The purpose is to check that all alignment params get
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	466 parsed correctly. -->
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	467 <param name="A" value="2" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	468 <param name="B" value="8" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	469 <param name="O" value="12" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	470 <param name="O2" value="32" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	471 <param name="E" value="2" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	472 <param name="E2" value="1" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	473 <param name="z" value="400" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	474 <param name="s" value="40" />
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	475 </section>
21 597f238f2b4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243" iuc parents: 20 diff changeset	476 <section name="io_options">
597f238f2b4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243" iuc parents: 20 diff changeset	477 <!-- the next setting is a noop for bam output, but tests that
597f238f2b4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243" iuc parents: 20 diff changeset	478 a valid command line is formed for the cs option -->
597f238f2b4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243" iuc parents: 20 diff changeset	479 <param name="cs" value="none" />
597f238f2b4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243" iuc parents: 20 diff changeset	480 </section>
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	481 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
16 fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	482 </test>
fd3673a18ad3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" iuc parents: 15 diff changeset	483 <test>
11 5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	484 <!-- test paf output -->
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	485 <param name="reference_source_selector" value="history" />
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	486 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" />
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	487 <param name="fastq_input_selector" value="single"/>
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	488 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" />
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	489 <param name="analysis_type_selector" value="ava-ont"/>
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	490 <param name="output_format" value="paf"/>
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	491 <output name="alignment_output" ftype="tabular" file="mini_reads.paf" />
5c73cef26bbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 iuc parents: 10 diff changeset	492 </test>
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	493 <test>
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	494 <!-- test self-homology mode -->
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	495 <param name="reference_source_selector" value="history" />
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	496 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	497 <param name="fastq_input_selector" value="single" />
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	498 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	499 <param name="analysis_type_selector" value="self-homology" />
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	500 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" />
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	501 </test>
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	502 <test>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	503 <!-- test mask-len option -->
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	504 <param name="reference_source_selector" value="history" />
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	505 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	506 <param name="fastq_input_selector" value="single"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	507 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	508 <param name="analysis_type_selector" value="sr"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	509 <section name="mapping_options">
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	510 <param name="mask_len" value="100"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	511 </section>
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	512 <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" />
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	513 </test>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	514 <test>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	515 <!-- test map-hifi -->
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	516 <param name="reference_source_selector" value="history" />
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	517 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	518 <param name="fastq_input_selector" value="single"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	519 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	520 <param name="analysis_type_selector" value="map-hifi"/>
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	521 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" />
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	522 </test>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	523 <test>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	524 <!-- test kmer ocurrence interval option -->
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	525 <param name="reference_source_selector" value="history" />
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	526 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	527 <param name="fastq_input_selector" value="single"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	528 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	529 <param name="analysis_type_selector" value="sr"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	530 <conditional name="kmer_ocurrence_interval">
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	531 <param name="interval" value="enabled"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	532 <param name="lower_limit" value="10"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	533 <param name="upper_limit" value="30"/>
11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	534 </conditional>
20 bb2c5a19ecbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8" iuc parents: 19 diff changeset	535 <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="4" />
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	536 </test>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	537 </tests>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	538 <help>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	539
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	540 Users’ Guide
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	541 ------------
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	542
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	543 Minimap2 is a versatile sequence alignment program that aligns DNA or
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	544 mRNA sequences against a large reference database. Typical use cases
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	545 include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	546 human genome; (2) finding overlaps between long reads with error rate up
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	547 to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	548 or Direct RNA reads against a reference genome; (4) aligning Illumina
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	549 single- or paired-end reads; (5) assembly-to-assembly alignment; (6)
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	550 full-genome alignment between two closely related species with
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	551 divergence below ~15%.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	552
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	553 For ~10kb noisy reads sequences, minimap2 is tens of times faster than
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	554 mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	555 is more accurate on simulated long reads and produces biologically
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	556 meaningful alignment ready for downstream analyses. For >100bp Illumina
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	557 short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	558 as accurate on simulated data. Detailed evaluations are available from
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	559 the `minimap2 preprint`.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	560
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	561 General usage
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	562 ~~~~~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	563
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	564 Minimap2 seamlessly works with gzip’d FASTA and FASTQ formats as input.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	565 You don’t need to convert between FASTA and FASTQ or decompress gzip’d
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	566 files first.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	567
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	568 For the human reference genome, minimap2 takes a few minutes to generate
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	569 a minimizer index for the reference before mapping. To reduce indexing
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	570 time, you can optionally save the index with option -d and replace
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	571 the reference sequence file with the index file on the minimap2 command
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	572 line:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	573
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	574 *Importantly*, it should be noted that once you build the index,
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	575 indexing parameters such as -k, -w, -H and -I can’t be
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	576 changed during mapping. If you are running minimap2 for different data
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	577 types, you will probably need to keep multiple indexes generated with
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	578 different parameters. This makes minimap2 different from BWA which
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	579 always uses the same index regardless of query data types.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	580
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	581 Use cases
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	582 ~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	583
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	584 Minimap2 uses the same base algorithm for all applications. However, due
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	585 to the different data types it supports (e.g. short vs long reads; DNA
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	586 vs mRNA reads), minimap2 needs to be tuned for optimal performance and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	587 accuracy. It is usually recommended to choose a preset with option
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	588 -x, which sets multiple parameters at the same time. The default
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	589 setting is the same as ``map-ont``.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	590
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	591 Map long noisy genomic reads
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	592 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	593
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	594 The difference between ``map-pb`` and ``map-ont`` is that ``map-pb``
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	595 uses homopolymer-compressed (HPC) minimizers as seeds, while ``map-ont``
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	596 uses ordinary minimizers as seeds. Emperical evaluation suggests HPC
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	597 minimizers improve performance and sensitivity when aligning PacBio
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	598 reads, but hurt when aligning Nanopore reads.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	599
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	600 Map long mRNA/cDNA reads
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	601 ^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	602
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	603 There are different long-read RNA-seq technologies, including
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	604 tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	605 and Direct RNA-seq. They produce data of varying quality and properties.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	606 By default, ``-x splice`` assumes the read orientation relative to the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	607 transcript strand is unknown. It tries two rounds of alignment to infer
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	608 the orientation and write the strand to the ``ts`` SAM/PAF tag if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	609 possible. For Iso-seq, Direct RNA-seq and tranditional full-length
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	610 cDNAs, it would be desired to apply ``-u f`` to force minimap2 to
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	611 consider the forward transcript strand only. This speeds up alignment
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	612 with slight improvement to accuracy. For noisy Nanopore Direct RNA-seq
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	613 reads, it is recommended to use a smaller k-mer size for increased
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	614 sensitivity to the first or the last exons.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	615
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	616 It is worth noting that by default ``-x splice`` prefers
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	617 GT[A/G]..[C/T]AG over GT[C/T]..[A/G]AG, and then over other splicing
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	618 signals. Considering one additional base improves the junction accuracy
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	619 for noisy reads, but reduces the accuracy when aligning against the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	620 widely used SIRV control data. This is because SIRV does not honor the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	621 evolutionarily conservative splicing signal. If you are studying SIRV,
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	622 you may apply ``--splice-flank=no`` to let minimap2 only model GT..AG,
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	623 ignoring the additional base.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	624
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	625 Find overlaps between long reads
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	626 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	627
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	628 Similarly, ``ava-pb`` uses HPC minimizers while ``ava-ont`` uses
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	629 ordinary minimizers. It is usually not recommended to perform base-level
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	630 alignment in the overlapping mode because it is slow and may produce
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	631 false positive overlaps. However, if performance is not a concern, you
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	632 may try to add ``-a`` or ``-c`` anyway.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	633
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	634 Map short accurate genomic reads
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	635 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	636
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	637 When two read files are specified, minimap2 reads from each file in turn
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	638 and merge them into an interleaved stream internally. Two reads are
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	639 considered to be paired if they are adjacent in the input stream and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	640 have the same name (with the ``/[0-9]`` suffix trimmed if present).
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	641 Single- and paired-end reads can be mixed.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	642
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	643 Minimap2 does not work well with short spliced reads. There are many
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	644 capable RNA-seq mappers for short reads.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	645
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	646 Full genome/assembly alignment
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	647 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	648
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	649 For cross-species full-genome alignment, the scoring system needs to be
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	650 tuned according to the sequence divergence.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	651
14 4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	652 Self-homology map creation
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	653 ^^^^^^^^^^^^^^^^^^^^^^^^^^
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	654
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	655 A self-homology map is created by mapping a genome (e.g. that of E. coli)
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	656 against itself. When this option is used the same FASTA file should
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	657 be used for reference and for the (single ended mode) query.
4f88b74199bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" iuc parents: 13 diff changeset	658
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	659 Advanced features
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	660 ~~~~~~~~~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	661
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	662 Working with >65535 CIGAR operations
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	663 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	664
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	665 Due to a design flaw, BAM does not work with CIGAR strings with >65535
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	666 operations (SAM and CRAM work). However, for ultra-long nanopore reads
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	667 minimap2 may align ~1% of read bases with long CIGARs beyond the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	668 capability of BAM. If you convert such SAM/CRAM to BAM, Picard and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	669 recent samtools will throw an error and abort. Older samtools and other
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	670 tools may create corrupted BAM.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	671
8 6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	672 To avoid this issue, you can add option ``-L`` at the minimap2 command line.
6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	673 This option moves a long CIGAR to the ``CG`` tag and leaves a fully clipped
6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	674 CIGAR at the SAM CIGAR column. Current tools that don’t read CIGAR
6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	675 (e.g. merging and sorting) still work with such BAM records; tools that read
6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	676 CIGAR will effectively ignore these records. It has been decided that future
6090793a47e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739 iuc parents: 7 diff changeset	677 tools will seamlessly recognize long-cigar records generated by option `-L`.
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	678
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	679 TD;DR: if you work with ultra-long reads and use tools that only
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	680 process BAM files, please add option ``-L``.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	681
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	682 The cs optional tag
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	683 ^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	684
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	685 The ``cs`` SAM/PAF tag encodes bases at mismatches and INDELs. It
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	686 matches regular expression
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	687 ``/(:[0-9]+\|\*[a-z][a-z]\|[=\+\-][A-Za-z]+)+/``. Like CIGAR, ``cs``
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	688 consists of series of operations. Each leading character specifies the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	689 operation; the following sequence is the one involved in the operation.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	690
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	691 The ``cs`` tag is enabled by command line option ``--cs``. The following
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	692 alignment, for example:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	693
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	694 .. code::
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	695
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	696 CGATCGATAAATAGAGTAG---GAATAGCA
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	697 \|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	698 CGATCG---AATAGAGTAGGTCGAATtGCA
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	699
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	700 is represented as ``:6-ata:10+gtc:4*at:3``, where ``:[0-9]+`` represents
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	701 an identical block, ``-ata`` represents a deltion, ``+gtc`` an insertion
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	702 and ``*at`` indicates reference base ``a`` is substituted with a query
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	703 base ``t``. It is similar to the ``MD`` SAM tag but is standalone and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	704 easier to parse.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	705
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	706 If ``--cs=long`` is used, the ``cs`` string also contains identical
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	707 sequences in the alignment. The above example will become
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	708 ``=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA``. The long form of ``cs``
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	709 encodes both reference and query sequences in one string.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	710
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	711 Algorithm overview
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	712 ~~~~~~~~~~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	713
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	714 In the following, minimap2 command line options have a dash ahead and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	715 are highlighted in bold. The description may help to tune minimap2
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	716 parameters.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	717
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	718 1. Read -I [=4G] reference bases, extract
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	719 (-k,\ -w)-minimizers and index them in a hash table.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	720
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	721 2. Read -K [=200M] query bases. For each query sequence, do step 3
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	722 through 7:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	723
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	724 3. For each (-k,\ -w)-minimizer on the query, check against the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	725 reference index. If a reference minimizer is not among the top -f
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	726 [=2e-4] most frequent, collect its the occurrences in the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	727 reference, which are called seeds.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	728
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	729 4. Sort seeds by position in the reference. Chain them with dynamic
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	730 programming. Each chain represents a potential mapping. For read
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	731 overlapping, report all chains and then go to step 8. For reference
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	732 mapping, do step 5 through 7:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	733
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	734 5. Let P be the set of primary mappings, which is an empty set
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	735 initially. For each chain from the best to the worst according to
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	736 their chaining scores: if on the query, the chain overlaps with a
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	737 chain in P by –mask-level [=0.5] or higher fraction of the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	738 shorter chain, mark the chain as secondary to the chain in P;
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	739 otherwise, add the chain to P.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	740
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	741 6. Retain all primary mappings. Also retain up to -N [=5] top
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	742 secondary mappings if their chaining scores are higher than -p
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	743 [=0.8] of their corresponding primary mappings.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	744
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	745 7. If alignment is requested, filter out an internal seed if it
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	746 potentially leads to both a long insertion and a long deletion.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	747 Extend from the left-most seed. Perform global alignments between
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	748 internal seeds. Split the chain if the accumulative score along the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	749 global alignment drops by -z [=400], disregarding long gaps.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	750 Extend from the right-most seed. Output chains and their alignments.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	751
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	752 8. If there are more query sequences in the input, go to step 2 until no
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	753 more queries are left.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	754
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	755 9. If there are more reference sequences, reopen the query file from the
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	756 start and go to step 1; otherwise stop.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	757
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	758 Limitations
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	759 -----------
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	760
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	761 - Minimap2 may produce suboptimal alignments through long
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	762 low-complexity regions where seed positions may be suboptimal. This
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	763 should not be a big concern because even the optimal alignment may be
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	764 wrong in such regions.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	765 </help>
19 11ef1ee4282c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852" iuc parents: 18 diff changeset	766 <expand macro="citations"/>
0 9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	767 </tool>

Mercurial > repos > iuc > minimap2

annotate minimap2.xml @ 22:b81d44caa1a0 draft