minimap2: minimap2.xml annotate

annotate minimap2.xml @ 0:9b44afd426fd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty

author	iuc
date	Fri, 03 Nov 2017 16:57:51 -0400
parents
children	acb6d016cabe

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"?>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	2 <tool id="minimap2" name="Map with minimap2" version="2.3" profile="17.01">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	3 <description>- A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	4 <requirements>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	5 <requirement type="package" version="2.3">minimap2</requirement>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	6 <requirement type="package" version="1.6">samtools</requirement>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	7 </requirements>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	8 <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	9 <command>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	10 <![CDATA[
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	11 ln -f -s '$reference_source.ref_file' reference.fa &&
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	12 minimap2 -a
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	13 -x $analysis_type_selector
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	14 ## indexing options
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	15 #if $indexing_options.k:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	16 -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	17 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	18 #if $indexing_options.w:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	19 -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	20 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	21 #if $indexing_options.I:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	22 -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	23 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	24 ## Mapping options
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	25 #if $mapping_options.f:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	26 -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	27 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	28 #if $mapping_options.g:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	29 -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	30 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	31 #if $mapping_options.G:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	32 -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	33 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	34 #if $mapping_options.F:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	35 -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	36 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	37 #if $mapping_options.r:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	38 -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	39 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	40 #if $mapping_options.n:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	41 -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	42 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	43 #if $mapping_options.m:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	44 -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	45 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	46 $mapping_options.X
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	47 #if $mapping_options.p:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	48 -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	49 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	50 #if $mapping_options.N:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	51 -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	52 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	53 ## Alignment options
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	54 #if $alignment_options.A:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	55 -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	56 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	57 #if $alignment_options.B:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	58 -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	59 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	60 #if $alignment_options.O:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	61 -O $alignment_options.O
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	62 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	63 #if $alignment_options.E:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	64 -E $alignment_options.E
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	65 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	66 #if $alignment_options.z:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	67 $alignment_options.z
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	68 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	69 #if $alignment_options.s:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	70 -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	71 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	72 #if $alignment_options.u:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	73 -u $alignment_options.u
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	74 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	75 ## Output options
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	76 $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	77 $io_options.L
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	78 #if $io_options.cs:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	79 --cs $io_options.cs
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	80 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	81 #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	82 -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	83 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	84 -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	85 reference.fa
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	86 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	87 '$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	88 #else if $fastq_input.fastq_input_selector == 'paired':
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	89 '$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	90 #else if $fastq_input.fastq_input_selector == 'paired_collection':
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	91 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input2.reverse'
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	92 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	93 \| samtools sort
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	94 -@\${GALAXY_SLOTS:-2}
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	95 -O BAM
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	96 #if $io_options.output_format == 'CRAM':
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	97 -l 0\| samtools view -T reference.fa -C
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	98 #end if
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	99 > '$alignment_output'
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	100 ]]>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	101 </command>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	102 <inputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	103 <conditional name="reference_source">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	104 <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">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	105 <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	106 <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	107 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	108 <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	109 <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	110 <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	111 <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	112 <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	113 </options>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	114 <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	115 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	116 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	117 <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	118 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	119 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	120 </conditional>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	121 <section name="indexing_options" title="Indexing options">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	122 <!-- Homopolymer setting seems to not properly overwrite sr preset
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	123 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	124 -->
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	125 <param argument="-k" type="integer" min="4" max="28" optional="true" label="k-mer size" help=""/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	126 <param argument="-w" type="integer" min="1" optional="true" label="minimizer window size" help=""/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	127 <param argument="-I" type="integer" min="1" optional="true" label="split index for every N input gigabases" help=""/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	128 </section>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	129 <!-- 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	130 <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	131 <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	132 <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	133 <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	134 <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	135 <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	136 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	137 <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	138 <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	139 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	140 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	141 <when value="single">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	142 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	143 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	144 <when value="paired_collection">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	145 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	146 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	147 <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	148 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	149 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	150 </conditional>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	151 <!-- end unchanged copy from bwa-mem -->
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	152 <param name="analysis_type_selector" type="select" label="Select analysis mode (sets default)">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	153 <option value="map-pb">-Hk19 (PacBio vs reference mapping)</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	154 <option value="map-ont">-k15 (Oxford Nanopore vs reference mapping)</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	155 <option value="asm5">-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5% div.)</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	156 <option value="asm10">-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10% div.)</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	157 <option value="ava-pb">-Hk19 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (PacBio read overlap)</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	158 <option value="ava-ont">-k15 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (ONT read overlap)</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	159 <option value="splice">long-read spliced alignment</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	160 <option value="sr">short single-end reads without splicing</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	161 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	162 <section name="mapping_options" title="Set advanced mapping options" help="Sets -f, -g, -G, -F, -r, -n, -m, -X, -p, and -N options." expanded="False">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	163 <param argument="-f" type="float" value="" optional="true" label="filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	164 <param argument="-g" type="integer" value="" optional="true" label="stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	165 <param argument="-G" type="integer" value="" optional="true" label="max intron length in thousand (effective with -xsplice; changing -r)" help="default=200"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	166 <param argument="-F" type="integer" value="" optional="true" label="max fragment length (effective with -xsr or in the fragment mode)" help="default=800" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	167 <param argument="-r" type="integer" value="" optional="true" label="bandwidth used in chaining and DP-based alignment" help="default=500" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	168 <param argument="-n" type="integer" value="" optional="true" label="minimal number of minimizers on a chain" help="default=3"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	169 <param argument="-m" type="integer" value="" optional="true" label="minimal chaining score (matching bases minus log gap penalty)" help="default=40"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	170 <param argument="-X" type="boolean" truevalue="-X" falsevalue="" optional="true" label="skip self and dual mappings (for the all-vs-all mode)"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	171 <param argument="-p" type="float" value="" max="1" optional="true" label="min secondary-to-primary score ratio" help="default=0.8"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	172 <param argument="-N" type="integer" min="0" optional="true" label="retain at most INT secondary alignments" help="default=5"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	173 </section>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	174 <section name="alignment_options" title="Set advanced alignment options" help="Sets -Q, -L, -R, -c, --cs, and -K options." expanded="False">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	175 <param argument="-A" type="integer" optional="true" label="Score for a sequence match" help="default=2"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	176 <param argument="-B" type="integer" optional="true" label="Penalty for a mismatch" help="-B; default=4" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	177 <param argument="-O" type="text" optional="true" label="Gap open penalties for deletions and insertions" help="-O; default=4,24">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	178 <sanitizer invalid_char="">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	179 <valid initial="string.digits"><add value=","/> </valid>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	180 </sanitizer>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	181 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	182 <param argument="-E" type="text" optional="true" label="Gap extension penalties; a gap of size k cost '-O + -E*k'. If two numbers are specified, the first is the penalty of extending a deletion and the second for extending an insertion" help="-E; default=2,1">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	183 <sanitizer invalid_char="">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	184 <valid initial="string.digits"><add value=","/> </valid>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	185 </sanitizer>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	186 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	187 <param argument="-z" type="integer" optional="true" label="Z-drop score" help="default=400"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	188 <param argument="-s" type="integer" optional="true" label="minimal peak DP alignment score" help="default=80"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	189 <param argument="-u" type="select" optional="true" label="how to find GT-AG">
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	190 <option value="n">don't match GT-AG</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	191 <option value="f">transcript strand</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	192 <option value="b">both strands</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	193 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	194 </section>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	195 <section name="io_options" title="Set advanced output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options." expanded="False">
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="output_format" type="select" label="Produce BAM or CRAM file?">
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="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	198 <option value="CRAM">CRAM</option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	199 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	200 <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" optional="true" label="don't output base quality"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	201 <param argument="-L" type="boolean" truevalue="-L" falsevalue="" optional="true" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	202 <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	203 <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	204 <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	205 <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	206 <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	207 </param>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	208 </section>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	209 </inputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	210 <outputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	211 <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	212 <actions>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	213 <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	214 <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	215 <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	216 <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	217 <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	218 <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	219 </option>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	220 </action>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	221 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	222 <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	223 <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	224 <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	225 </action>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	226 </when>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	227 </conditional>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	228 </actions>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	229 <change_format>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	230 <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	231 </change_format>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	232 </data>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	233 </outputs>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	234 <tests>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	235 <test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	236 <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	237 <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	238 <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	239 <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	240 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	241 <param name="analysis_type_selector" value="sr"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	242 <output name="alignment_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	243 </test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	244 <test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	245 <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	246 <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	247 <param name="fastq_input_selector" value="single"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	248 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	249 <param name="analysis_type_selector" value="sr"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	250 <output name="alignment_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="2" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	251 </test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	252 <test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	253 <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	254 <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	255 <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	256 <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	257 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	258 <param name="analysis_type_selector" value="sr"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	259 <output name="alignment_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	260 </test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	261 <test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	262 <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	263 <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	264 <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	265 <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	266 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	267 <param name="analysis_type_selector" value="sr"/>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	268 <output name="alignment_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="2" />
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	269 </test>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	270 </tests>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	271 <help>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	272
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	273 Users’ Guide
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	274 ------------
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	275
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	276 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	277 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	278 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	279 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	280 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	281 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	282 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	283 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	284 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	285
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	286 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	287 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	288 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	289 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	290 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	291 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	292 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	293
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	294 General usage
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	295 ~~~~~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	296
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	297 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	298 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	299 files first.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	300
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	301 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	302 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	303 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	304 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	305 line:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	306
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	307 *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	308 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	309 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	310 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	311 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	312 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	313
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	314 Use cases
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	315 ~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	316
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	317 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	318 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	319 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	320 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	321 -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	322 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	323
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	324 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	325 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	326
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	327 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	328 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	329 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	330 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	331 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	332
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	333 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	334 ^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	335
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	336
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	337 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	338 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	339 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	340 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	341 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	342 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	343 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	344 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	345 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	346 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	347 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	348 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	349
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	350 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	351 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	352 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	353 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	354 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	355 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	356 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	357 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	358
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	359 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	360 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	361
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	362 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	363 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	364 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	365 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	366 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	367
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	368 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	369 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	370
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	371
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	372 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	373 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	374 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	375 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	376 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	377
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	378 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	379 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	380
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	381 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	382 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	383
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	384 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	385 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	386
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	387 Advanced features
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	388 ~~~~~~~~~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	389
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	390 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	391 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	392
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	393 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	394 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	395 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	396 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	397 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	398 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	399
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	400 To avoid this issue, you can add option ``-L`` at 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	401 line. This option moves a long CIGAR to the ``CG`` tag and leaves a
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	402 fully clipped CIGAR at the SAM CIGAR column. Current tools that don’t
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	403 read CIGAR (e.g. merging and sorting) still work with such BAM records;
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	404 tools that read CIGAR will effectively ignore these records. I have pull
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	405 requests to the SAM spec, htslib, htsjdk, bedtools2, Rsamtools and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	406 igv.js. If they are accepted, future versions of these tools will
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	407 seamlessly recognize long-cigar records generated by option ``-L``.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	408
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	409 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	410 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	411
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	412 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	413 ^^^^^^^^^^^^^^^^^^^
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	414
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	415 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	416 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	417 ``/(:[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	418 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	419 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	420
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	421 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	422 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	423
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	424 .. code::
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	425
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	426 CGATCGATAAATAGAGTAG---GAATAGCA
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	427 \|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	428 CGATCG---AATAGAGTAGGTCGAATtGCA
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	429
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	430 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	431 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	432 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	433 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	434 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	435
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	436 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	437 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	438 ``=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	439 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	440
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	441 Algorithm overview
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	442 ~~~~~~~~~~~~~~~~~~
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	443
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	444 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	445 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	446 parameters.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	447
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	448 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	449 (-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	450
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	451 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	452 through 7:
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	453
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	454 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	455 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	456 [=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	457 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	458
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	459 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	460 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	461 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	462 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	463
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	464 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	465 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	466 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	467 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	468 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	469 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	470
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	471 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	472 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	473 [=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	474
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	475 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	476 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	477 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	478 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	479 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	480 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	481
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	482 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	483 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	484
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	485 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	486 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	487
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	488 Limitations
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	489 -----------
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	490
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	491 - 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	492 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	493 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	494 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	495
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	496 - Minimap2 requires SSE2 instructions to compile. It is possible to add
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	497 non-SSE2 support, but it would make minimap2 slower by several times.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	498
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	499 In general, minimap2 is a young project with most code written since
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	500 June, 2017. It may have bugs and room for improvements. Bug reports and
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	501 suggestions are warmly welcomed.
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	502 </help>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	503 <citations>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	504 <citation type="doi">10.1093/bioinformatics/btp324</citation>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	505 <citation type="doi">10.1093/bioinformatics/btp698</citation>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	506 <citation type="bibtex">@misc{1303.3997,
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	507 Author = {Heng Li},
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	508 Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	509 Year = {2017},
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	510 Eprint = {arXiv:1708.01492},
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	511 url = {https://arxiv.org/abs/1708.01492},
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	512 }</citation>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	513 </citations>
9b44afd426fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d467ba21d5a83a68e87625c9e9157b37eac03eda-dirty iuc parents: diff changeset	514 </tool>

Mercurial > repos > iuc > minimap2

annotate minimap2.xml @ 0:9b44afd426fd draft