winnowmap: winnowmap.xml annotate

annotate winnowmap.xml @ 1:44231ef8167a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit a8ec6c1845b23188ea18c459d8b0d9126498fecc"

author	iuc
date	Mon, 10 May 2021 19:28:32 +0000
parents	1c070debf549
children	35ea4a8b1ea6

rev	line source
0 1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	1 <tool id="winnowmap" name="Winnowmap" version="@TOOL_VERSION@+galaxy0" profile="20.01">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	2 <description>a mapping tool optimized for repetitive sequences</description>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	3 <macros>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	4 <import>macros.xml</import>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	5 </macros>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	6 <expand macro="edam_ontology"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	7 <expand macro="requirements"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	8 <stdio>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	9 <exit_code range="1:" level="fatal" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	10 <regex match="\[ERROR\]" source="stderr" level="fatal" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	11 </stdio>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	12 <version_command>winnowmap --version</version_command>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	13 <command>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	14 <![CDATA[
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	15 #if $reference_source.reference_source_selector == 'history':
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	16 ln -f -s '$reference_source.ref_file' reference.fa &&
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	17 #else:
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	18 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	19 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	20 winnowmap
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	21 #if str($analysis_type_selector) == 'self-homology':
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	22 -DP -k19 -w19 -m200
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	23 #elif $analysis_type_selector:
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	24 -x ${analysis_type_selector}
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	25 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	26 #if str($highfreq_kmers):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	27 -W $highfreq_kmers
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	28 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	29 ## indexing options
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	30 $indexing_options.H
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	31 #if str($indexing_options.k) and not str($highfreq_kmers):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	32 -k $indexing_options.k
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	33 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	34 #if str($indexing_options.w):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	35 -w $indexing_options.w
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	36 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	37 #if str($indexing_options.I):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	38 -I $indexing_options.I
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	39 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	40
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	41 ## Mapping options
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	42 #if str($mapping_options.f):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	43 -f $mapping_options.f
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	44 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	45 #if str($mapping_options.min_occ_floor):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	46 --min-occ-floor $mapping_options.min_occ_floor
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	47 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	48 #if str($mapping_options.g):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	49 -g $mapping_options.g
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	50 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	51 #if str($mapping_options.r):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	52 -r $mapping_options.r
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	53 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	54 #if str($mapping_options.n):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	55 -n $mapping_options.n
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	56 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	57 #if str($mapping_options.m):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	58 -m $mapping_options.m
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	59 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	60 #if str($mapping_options.max_chain_skip):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	61 --max-chain-skip $mapping_options.max_chain_skip
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	62 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	63 #if str($mapping_options.max_chain_iter):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	64 --max-chain-iter $mapping_options.max_chain_iter
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	65 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	66 $mapping_options.X
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	67 #if str($mapping_options.p):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	68 -p $mapping_options.p
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	69 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	70 #if str($mapping_options.sv_off):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	71 --sv-off
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	72 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	73
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	74 ## Alignment options
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	75 #if str($alignment_options.splicing.splice_mode) == '--splice':
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	76 --frag=no --splice
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	77 #if str($alignment_options.splicing.G):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	78 -G $alignment_options.splicing.G
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	79 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	80 #if str($alignment_options.splicing.C):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	81 -C $alignment_options.splicing.C
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	82 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	83 #if $alignment_options.splicing.u:
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	84 -u $alignment_options.splicing.u
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	85 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	86 $alignment_options.splicing.splice_flank
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	87 #if str($alignment_options.splicing.splice_site_annotations.use_annotations) == 'yes':
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	88 --junc-bed '$alignment_options.splicing.splice_site_annotations.junc_bed'
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	89 --junc-bonus $alignment_options.splicing.splice_site_annotations.junc_bonus
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	90 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	91 #elif str($mapping_options.F) and 'splice' not in str($analysis_type_selector):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	92 --frag=yes -F $mapping_options.F
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	93 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	94 #if str($alignment_options.A):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	95 -A $alignment_options.A
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	96 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	97 #if str($alignment_options.B):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	98 -B $alignment_options.B
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	99 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	100 #if str($alignment_options.O):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	101 #if str($alignment_options.O2):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	102 -O $alignment_options.O,$alignment_options.O2
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	103 #else
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	104 -O $alignment_options.O
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	105 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	106 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	107 #if str($alignment_options.E):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	108 #if str($alignment_options.E2):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	109 -E $alignment_options.E,$alignment_options.E2
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	110 #else
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	111 -E $alignment_options.E
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	112 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	113 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	114 #if str($alignment_options.z):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	115 #if str($alignment_options.z2):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	116 -z $alignment_options.z,$alignment_options.z2
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	117 #else
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	118 -z $alignment_options.z
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	119 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	120 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	121 #if str($alignment_options.s):
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	122 -s $alignment_options.s
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	123 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	124 $alignment_options.no_end_flt
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	125 ## Output options
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	126 $io_options.Q
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	127 $io_options.L
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	128 $io_options.c
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	129 #if $io_options.cs:
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	130 --cs $io_options.cs
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	131 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	132 $io_options.Y
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	133 #if $io_options.K:
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	134 -K $io_options.K
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	135 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	136 -t \${GALAXY_SLOTS:-4}
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	137 reference.fa
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	138 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	139 '$fastq_input.fastq_input1'
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	140 #else if $fastq_input.fastq_input_selector == 'paired':
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	141 '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	142 #else if $fastq_input.fastq_input_selector == 'paired_collection':
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	143 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	144 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	145 #if $io_options.output_format == 'BAM':
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	146 -a
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	147 \| samtools sort
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	148 -@\${GALAXY_SLOTS:-2}
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	149 -T "\${TMPDIR:-.}"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	150 -O $io_options.output_format
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	151 -o '$alignment_output'
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	152 #else if $io_options.output_format == 'CRAM':
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	153 -a
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	154 \| samtools sort
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	155 -T "\${TMPDIR:-.}"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	156 -@\${GALAXY_SLOTS:-2}
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	157 -O $io_options.output_format
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	158 $io_options.eqx
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	159 --reference reference.fa
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	160 --output-fmt-option no_ref
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	161 -o '$alignment_output'
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	162 #else:
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	163 > '$alignment_output'
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	164 #end if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	165 ]]>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	166 </command>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	167 <inputs>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	168 <conditional name="reference_source">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	169 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	170 <option value="cached">Use a built-in genome index</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	171 <option value="history">Use a genome from history and build index</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	172 </param>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	173 <when value="cached">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	174 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	175 <options from_data_table="all_fasta">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	176 <filter type="sort_by" column="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	177 <validator type="no_options" message="No reference genomes are available" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	178 </options>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	179 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	180 </param>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	181 </when>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	182 <when value="history">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	183 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	184 </when>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	185 </conditional>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	186 <!-- start unchanged copy from bwa-mem -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	187 <conditional name="fastq_input">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	188 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	189 <option value="single">Single</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	190 <option value="paired">Paired</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	191 <option value="paired_collection">Paired Collection</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	192 <option value="paired_iv">Paired Interleaved</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	193 </param>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	194 <!-- below, preset options are only offered for single-end input
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	195 because paired-end alignment in minimap2 is only enabled with -x sr
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	196 (see https://github.com/lh3/minimap2/issues/190) -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	197 <when value="single">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	198 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	199 </when>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	200 <when value="paired">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	201 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	202 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	203 </when>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	204 <when value="paired_collection">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	205 <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"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	206 </when>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	207 <when value="paired_iv">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	208 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	209 </when>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	210 </conditional>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	211 <param name="highfreq_kmers" argument="-W" type="data" format="tabular" label="High frequency k-mers dataset" optional="True" help="Input file containing list of high freq. k-mers generated by meryl"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	212 <param name="analysis_type_selector" type="select" optional="True"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	213 label="Select a profile of preset options"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	214 help="Each profile comes with the preconfigured settings mentioned in parentheses. You can customize each profile further in the indexing, mapping and alignment options sections below. If you do not select a profile here, the tool will use the per-parameter defaults listed in the below sections unless you customize them." >
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	215 <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19) (map-pb)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	216 <option value="map-ont">Oxford Nanopore read to reference mapping. Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For PacBio reads, HPC minimizers consistently leads to faster performance and more sensitive results in comparison to normal minimizers. For Oxford Nanopore data, normal minimizers are better, though not much. The effectiveness of HPC is determined by the sequencing error mode. (map-ont)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	217 <option value="map-pb-clr">Turn off SV-aware mode for (relatively) short and noisy reads (map-pb-ctr)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	218 <option value="asm5">Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%. (asm5)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	219 <option value="asm10">Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 10% sequence divergence. (asm10)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	220 <option value="asm20">Long assembly to reference mapping (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence. (asm20)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	221 <option value="splice">Long-read spliced alignment (-k15 -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as the `N' CIGAR operator 2) long insertions are disabled 3) deletion and insertion gap costs are different during chaining 4) the computation of the `ms` tag ignores introns to demote hits to pseudogenes. (splice)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	222 <option value="splice:hq">Long-read splice alignment for PacBio CCS reads (same as `splice` but with -C5 -O6,24 -B4) (splice:hq)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	223 <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200) (self-homology)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	224 </param>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	225 <section name="indexing_options" title="Indexing options">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	226 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	227 <param argument="-k" type="integer" min="4" max="28" optional="true" label="K-mer size" help="k-mer size (no larger than 28). "/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	228 <param argument="-w" type="integer" min="1" optional="true" label="Minimizer window size" help=""/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	229 <param argument="-I" type="integer" min="1" optional="true" label="Split index for every N input gigabases" help=""/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	230 </section>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	231 <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, --sv-off and --min-occ-floor options." expanded="False">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	232 <param name="sv_off" argument="--sv-off" type="boolean" truevalue="--sv-off" falsevalue="" checked="False" label="Turn off SV-aware mode" help="SV aware k-mer search allows to find approximate mapping locations for a read"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	233 <param argument="-F" type="integer" min="0" value="" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	234 label="Max fragment length for PE alignment"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	235 help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	236 <param argument="-f" type="float" value="" optional="true" label="Filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	237 <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="Force winnowmap to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	238 <param argument="-g" type="integer" value="" optional="true" label="Stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	239 <param argument="-r" type="integer" value="" optional="true" label="Bandwidth used in chaining and DP-based alignment" help="default=500" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	240 <param argument="-n" type="integer" value="" optional="true" label="Minimal number of minimizers on a chain" help="default=3"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	241 <param argument="-m" type="integer" value="" optional="true" label="Minimal chaining score (matching bases minus log gap penalty)" help="default=40"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	242 <param argument="--max-chain-skip" type="integer" value="" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	243 label="Maximum seed skips during chaining"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	244 help="A heuristics that stops chaining early. Winnowmap uses dynamic programming for chaining. The time complexity is quadratic in the number of seeds. This option makes winnowmap exit the inner loop if it repeatedly sees seeds already on chains. Set to a large number to switch off this heurstics effectively. default=25" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	245 <param argument="--max-chain-iter" type="integer" value="" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	246 label="Maximum number of partial chains checked during chaining"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	247 help="A heuristics to avoid quadratic time complexity in the worst case. default=5000" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	248 <param argument="-X" type="boolean" truevalue="-X" falsevalue="" optional="true" label="Skip self and dual mappings (for the all-vs-all mode)"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	249 <param argument="-p" type="float" value="" max="1" optional="true" label="Min secondary-to-primary score ratio" help="default=0.8"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	250 </section>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	251 <section name="alignment_options" title="Alignment options" help="Sets -A, -B, -O, -E, -z, -s, and spliced alignments options." expanded="False">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	252 <conditional name="splicing">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	253 <param name="splice_mode" type="select"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	254 label="Customize spliced alignment mode?"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	255 help="Warning: Winnowmap cannot currently perform spliced alignments of read pairs. If you enable spliced alignment for paired-end data it will be treated as single-end!" >
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	256 <option value="preset">No, use profile setting or leave turned off</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	257 <option value="">Disable spliced alignments (overwrite profile setting if necessary)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	258 <option value="--splice">Yes, enable spliced alignments (--splice)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	259 </param>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	260 <when value="preset" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	261 <when value="" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	262 <when value="--splice">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	263 <param argument="-G" type="integer" value="" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	264 label="Maximum allowed gap on the reference"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	265 help="Higher values cause slower spliced alignment. When in use, this option causes -r (in mapping options) to be set to the same value. default=200k" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	266 <param argument="-C" type="integer" min="0" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	267 label="Cost of non-canonical (non-GT-AG) splicing"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	268 help="default=0" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	269 <param argument="-u" type="select" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	270 label="how to find GT-AG"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	271 help="default=n (don't match GT-AG)">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	272 <option value="n">don't match GT-AG (-un)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	273 <option value="f">transcript strand (-uf)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	274 <option value="b">both strands (-ub)</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	275 </param>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	276 <param argument="--splice-flank" type="boolean" truevalue="--splice-flank=yes" falsevalue="--splice-flank=no" checked="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	277 label="Assume conserved flanking region of splice sites?"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	278 help="Assume the next base to a GT donor site tends to be A/G (91% in human and 92% in mouse) and the preceding base to a AG acceptor tends to be C/T. This trend is evolutionarily conserved, all the way to S. cerevisiae (PMID:18688272). Specifying this option generally leads to higher junction accuracy by several percents, so it is applied by default with --splice. However, the SIRV control does not honor this trend (only ~60%) so this option reduces accuracy. If you are benchmarking winnowmap on SIRV data, please disable this option." />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	279 <conditional name="splice_site_annotations">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	280 <param name="use_annotations" type="select"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	281 label="Use previously annotated splice sites to guide the alignment?"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	282 help="">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	283 <option value="no">No, perform unbiased alignment</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	284 <option value="yes">Yes, favor annotated splice sites</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	285 </param>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	286 <when value="no" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	287 <when value="yes">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	288 <param argument="--junc-bed" type="data" format="bed"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	289 label="Dataset with annotated genes or introns"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	290 help="Gene annotations should be provided in BED12 (aka 12-column BED), intron positions in 5-column BED format." />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	291 <param argument="--junc-bonus" type="integer" min="1" value="1"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	292 label="Annotated splice site bonus"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	293 help="Score bonus for a splice donor or acceptor found in annotation." />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	294 </when>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	295 </conditional>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	296 </when>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	297 </conditional>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	298 <param argument="-A" type="integer" min="0" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	299 label="Score for a sequence match" help="default=2"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	300 <param argument="-B" type="integer" min="0" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	301 label="Penalty for a mismatch" help="-B; default=4" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	302 <param argument="-O" type="integer" min="1" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	303 label="Gap open penalties for deletions" help="-O; default=4"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	304 <param name="O2" type="integer" min="0" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	305 label="Gap open penalties for insertions" help="-O; default=24"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	306 <param argument="-E" type="integer" min="1" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	307 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"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	308 help="-E; default=2"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	309 <param name="E2" type="integer" min="0" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	310 label="Gap extension penalty for extending an insertion; if left empty uses the value specified for Gap extension penalties above"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	311 help="-E; default=1"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	312 <param argument="-z" type="integer" min="0" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	313 label="Z-drop threshold for truncating an alignment"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	314 help="Increase to improve the contiguity of alignments at the cost of poorer alignments in the middle. default=400" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	315 <param name="z2" type="integer" min="0" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	316 label="Z-drop threshold for reverse-complementing the query"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	317 help="Decrease to find small inversions at the cost of performance and false positives. default=200" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	318 <param argument="-s" type="integer" min="0" optional="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	319 label="minimal peak DP alignment score" help="default=80"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	320 <param name="no_end_flt" type="boolean" falsevalue="--no-end-flt" truevalue="" checked="true"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	321 label="Filter seeds towards the ends of chains before performing base-level alignment?" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	322 </section>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	323 <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	324 <param name="output_format" type="select" label="Select an output format">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	325 <option value="BAM">BAM</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	326 <option value="CRAM">CRAM</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	327 <option value="paf">paf</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	328 </param>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	329 <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" label="don't output base quality"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	330 <param argument="-L" type="boolean" truevalue="-L" falsevalue="" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	331 <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	332 <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.">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	333 <option value="none">no</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	334 <option value="short">short</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	335 <option value="long">long</option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	336 </param>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	337 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Generate CIGAR"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	338 help="In PAF, the CIGAR is written to the ‘cg’ custom tag." />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	339
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	340 <param argument="--eqx" type="boolean" truevalue="--eqx" falsevalue="" label="write =/X CIGAR operators"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	341 <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	342 </section>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	343 </inputs>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	344 <outputs>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	345 <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	346 <actions>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	347 <conditional name="reference_source.reference_source_selector">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	348 <when value="cached">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	349 <action type="metadata" name="dbkey">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	350 <option type="from_data_table" name="all_fasta" column="1" offset="0">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	351 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	352 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	353 </option>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	354 </action>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	355 </when>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	356 <when value="history">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	357 <action type="metadata" name="dbkey">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	358 <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	359 </action>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	360 </when>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	361 </conditional>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	362 </actions>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	363 <change_format>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	364 <when input="io_options.output_format" value="paf" format="tabular" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	365 <when input="io_options.output_format" value="CRAM" format="cram" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	366 </change_format>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	367 </data>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	368 </outputs>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	369 <tests>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	370 <test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	371 <!-- test single input -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	372 <param name="reference_source_selector" value="history" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	373 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	374 <param name="fastq_input_selector" value="single"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	375 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	376 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	377 <param name="analysis_type_selector" value="map-ont"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	378 <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	379 </test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	380 <test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	381 <!-- test cram output -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	382 <param name="reference_source_selector" value="history" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	383 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	384 <param name="fastq_input_selector" value="single"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	385 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	386 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	387 <param name="analysis_type_selector" value="map-ont"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	388 <param name="output_format" value="CRAM"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	389 <output name="alignment_output" ftype="cram" file="winnowmap-test1-fasta.cram" compare="sim_size" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	390 </test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	391 <test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	392 <!-- test paired input -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	393 <param name="reference_source_selector" value="history" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	394 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	395 <param name="fastq_input_selector" value="paired"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	396 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	397 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	398 <param name="analysis_type_selector" value="map-ont"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	399 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	400 <output name="alignment_output" ftype="bam" file="winnowmap-test1.bam" lines_diff="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	401 </test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	402 <test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	403 <!-- test paired input with one pair compressed -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	404 <param name="reference_source_selector" value="history" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	405 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	406 <param name="fastq_input_selector" value="paired"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	407 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	408 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	409 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	410 <param name="analysis_type_selector" value="map-ont"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	411 <output name="alignment_output" ftype="bam" file="winnowmap-test1.bam" lines_diff="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	412 </test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	413 <test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	414 <!-- test collection input -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	415 <param name="reference_source_selector" value="history" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	416 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	417 <param name="fastq_input_selector" value="paired_collection"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	418 <param name="fastq_input1">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	419 <collection type="paired">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	420 <element name="forward" value="bwa-mem-fastq1.fq" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	421 <element name="reverse" value="bwa-mem-fastq2.fq" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	422 </collection>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	423 </param>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	424 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	425 <output name="alignment_output" ftype="bam" file="winnowmap-test2.bam" lines_diff="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	426 </test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	427 <test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	428 <!-- test data table reference -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	429 <param name="reference_source_selector" value="cached" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	430 <param name="ref_file" value="bwa-mem-mt-genome"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	431 <param name="fastq_input_selector" value="single"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	432 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	433 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	434 <param name="analysis_type_selector" value="map-ont"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	435 <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	436 </test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	437 <test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	438 <!-- test alignment options -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	439 <param name="reference_source_selector" value="cached" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	440 <param name="min_occ_floor" value="1000"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	441 <param name="ref_file" value="bwa-mem-mt-genome"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	442 <param name="fastq_input_selector" value="single"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	443 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	444 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	445 <param name="analysis_type_selector" value="map-ont"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	446 <section name="alignment_options">
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	447 <!-- the folowing settings correspond to the defaults for "sr"
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	448 mode. The purpose is to check that all alignment params get
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	449 parsed correctly. -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	450 <param name="A" value="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	451 <param name="B" value="8" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	452 <param name="O" value="12" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	453 <param name="O2" value="32" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	454 <param name="E" value="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	455 <param name="E2" value="1" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	456 <param name="z" value="400" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	457 <param name="s" value="40" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	458 </section>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	459 <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	460 </test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	461 <test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	462 <!-- test paf output -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	463 <param name="reference_source_selector" value="history" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	464 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	465 <param name="fastq_input_selector" value="single"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	466 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	467 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	468 <param name="analysis_type_selector" value="map-ont"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	469 <param name="output_format" value="paf"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	470 <output name="alignment_output" ftype="tabular" file="mini_reads.paf" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	471 </test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	472 <test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	473 <!-- test self-homology mode -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	474 <param name="reference_source_selector" value="history" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	475 <param name="ref_file" ftype="fasta" value="winnowmap-self-homology.fasta" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	476 <param name="fastq_input_selector" value="single" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	477 <param name="fastq_input1" ftype="fasta" value="winnowmap-self-homology.fasta" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	478 <param name="analysis_type_selector" value="self-homology" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	479 <output name="alignment_output" ftype="bam" file="winnowmap-self-homology.bam" lines_diff="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	480 </test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	481 <test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	482 <!-- test sv_off parameter -->
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	483 <param name="reference_source_selector" value="history" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	484 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	485 <param name="fastq_input_selector" value="single"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	486 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	487 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	488 <param name="analysis_type_selector" value="map-ont"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	489 <param name="sv_off" value="True"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	490 <output name="alignment_output" ftype="bam" file="winnowmap-test2-fasta.bam" lines_diff="2" />
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	491 </test>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	492 </tests>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	493 <help>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	494
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	495 Users’ Guide
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	496 ------------
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	497
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	498 Winnowmap is a long-read mapping algorithm optimized for mapping ONT and
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	499 PacBio reads to repetitive reference sequences. Winnowmap development began
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	500 on top of minimap2 codebase, and since then we have incorporated the
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	501 following two ideas to improve mapping accuracy within repeats.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	502
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	503 Winnowmap implements a novel weighted minimizer sampling algorithm (>=v1.0).
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	504 This optimization was motivated by the need to avoid masking of frequently
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	505 occurring k-mers during the seeding stage in an efficient manner, and achieve
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	506 better mapping accuracy in complex repeats (e.g., long tandem repeats) of
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	507 the human genome. Using weighted minimizers, Winnowmap down-weights
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	508 frequently occurring k-mers, thus reducing their chance of getting selected
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	509 as minimizers. Users can refer to this paper for more details. This idea is
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	510 helpful to preserve the theoretical guarantee of minimizer sampling technique,
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	511 i.e., if two sequences share a substring of a specified length, then they
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	512 must be guaranteed to have a matching minimizer.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	513
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	514 We noticed that the highest scoring alignment doesn't necessarily correspond
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	515 to correct placement of reads in repetitive regions of T2T human chromosomes.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	516 In the presence of a non-reference allele within a repeat, a read sampled
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	517 from that region could be mapped to an incorrect repeat copy because the
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	518 standard pairwise sequence alignment scoring system penalizes true variants.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	519 This is also sometimes referred to as allelic bias. To address this bias,
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	520 we introduced and implemented an idea of using minimal confidently alignable
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	521 substrings (>=v2.0). These are minimal-length substrings in a read that align
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	522 end-to-end to a reference with mapping quality score above a user-specified
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	523 threshold. This approach treats each read mapping as a collection of
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	524 confident sub-alignments, which is more tolerant of structural variation
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	525 and more sensitive to paralog-specific variants (PSVs). Our most recent
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	526 paper desribes this concept and benchmarking results.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	527
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	528 General usage
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	529 ~~~~~~~~~~~~~
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	530
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	531 For either mapping long reads or computing whole-genome alignments, Winnowmap
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	532 requires pre-computing high frequency k-mers (e.g., top 0.02% most frequent)
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	533 in a reference. Winnowmap uses meryl k-mer counting tool for this purpose.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	534
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	535 Mapping ONT or PacBio-hifi WGS reads
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	536
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	537
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	538 .. code::
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	539
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	540 meryl count k=15 output merylDB ref.fa
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	541 meryl print greater-than distinct=0.9998 merylDB > repetitive_k15.txt
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	542
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	543
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	544 .. code::
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	545
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	546 winnowmap -W repetitive_k15.txt -ax map-ont ref.fa ont.fq.gz > output.sam [OR]
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	547 winnowmap -W repetitive_k15.txt -ax map-pb ref.fa hifi.fq.gz > output.sam
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	548
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	549 Mapping genome assemblies
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	550
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	551
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	552 .. code::
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	553
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	554 meryl count k=19 output merylDB asm1.fa
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	555 meryl print greater-than distinct=0.9998 merylDB > repetitive_k19.txt
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	556
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	557
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	558 .. code::
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	559
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	560 winnowmap -W repetitive_k19.txt -ax asm20 asm1.fa asm2.fa > output.sam
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	561
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	562 For the genome-to-genome use case, it may be useful to visualize the dot plot. This perl script can be used to generate a dot plot from paf-formatted output. In both usage cases, pre-computing repetitive k-mers using meryl is quite fast, e.g., it typically takes 2-3 minutes for the human genome reference.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	563
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	564 Use cases
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	565 ~~~~~~~~~
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	566
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	567 Winnowmap uses the same base algorithm for all applications. However, due
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	568 to the different data types it supports, Winnowmap needs to be tuned for
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	569 optimal performance and accuracy. It is usually recommended to choose a
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	570 preset with option -x, which sets multiple parameters at the same
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	571 time. The default setting is the same as ``map-ont``.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	572
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	573 Map long noisy genomic reads
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	574 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	575
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	576 The difference between ``map-pb`` and ``map-ont`` is that ``map-pb``
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	577 uses homopolymer-compressed (HPC) minimizers as seeds, while ``map-ont``
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	578 uses ordinary minimizers as seeds. Emperical evaluation suggests HPC
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	579 minimizers improve performance and sensitivity when aligning PacBio
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	580 reads, but hurt when aligning Nanopore reads.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	581
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	582 Map long mRNA/cDNA reads
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	583 ^^^^^^^^^^^^^^^^^^^^^^^^
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	584
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	585 There are different long-read RNA-seq technologies, including
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	586 tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	587 and Direct RNA-seq. They produce data of varying quality and properties.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	588 By default, ``-x splice`` assumes the read orientation relative to the
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	589 transcript strand is unknown. It tries two rounds of alignment to infer
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	590 the orientation and write the strand to the ``ts`` SAM/PAF tag if
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	591 possible. For Iso-seq, Direct RNA-seq and tranditional full-length
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	592 cDNAs, it would be desired to apply ``-u f`` to force Winnowmap to
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	593 consider the forward transcript strand only. This speeds up alignment
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	594 with slight improvement to accuracy. For noisy Nanopore Direct RNA-seq
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	595 reads, it is recommended to use a smaller k-mer size for increased
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	596 sensitivity to the first or the last exons.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	597
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	598 It is worth noting that by default ``-x splice`` prefers
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	599 GT[A/G]..[C/T]AG over GT[C/T]..[A/G]AG, and then over other splicing
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	600 signals. Considering one additional base improves the junction accuracy
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	601 for noisy reads, but reduces the accuracy when aligning against the
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	602 widely used SIRV control data. This is because SIRV does not honor the
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	603 evolutionarily conservative splicing signal. If you are studying SIRV,
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	604 you may apply ``--splice-flank=no`` to let Winnowmap only model GT..AG,
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	605 ignoring the additional base.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	606
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	607
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	608 Map short accurate genomic reads
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	609 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	610
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	611 When two read files are specified, Winnowmap reads from each file in turn
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	612 and merge them into an interleaved stream internally. Two reads are
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	613 considered to be paired if they are adjacent in the input stream and
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	614 have the same name (with the ``/[0-9]`` suffix trimmed if present).
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	615 Single- and paired-end reads can be mixed.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	616
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	617 Winnowmap does not work well with short spliced reads. There are many
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	618 capable RNA-seq mappers for short reads.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	619
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	620 Full genome/assembly alignment
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	621 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	622
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	623 For cross-species full-genome alignment, the scoring system needs to be
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	624 tuned according to the sequence divergence.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	625
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	626 Self-homology map creation
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	627 ^^^^^^^^^^^^^^^^^^^^^^^^^^
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	628
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	629 A self-homology map is created by mapping a genome (e.g. that of E. coli)
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	630 against itself. When this option is used the same FASTA file should
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	631 be used for reference and for the (single ended mode) query.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	632
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	633 Advanced features
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	634 ~~~~~~~~~~~~~~~~~
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	635
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	636 Working with >65535 CIGAR operations
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	637 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	638
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	639 Due to a design flaw, BAM does not work with CIGAR strings with >65535
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	640 operations (SAM and CRAM work). However, for ultra-long nanopore reads
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	641 Winnowmap may align ~1% of read bases with long CIGARs beyond the
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	642 capability of BAM. If you convert such SAM/CRAM to BAM, Picard and
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	643 recent samtools will throw an error and abort. Older samtools and other
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	644 tools may create corrupted BAM.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	645
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	646 To avoid this issue, you can add option ``-L`` at the Winnowmap command line.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	647 This option moves a long CIGAR to the ``CG`` tag and leaves a fully clipped
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	648 CIGAR at the SAM CIGAR column. Current tools that don’t read CIGAR
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	649 (e.g. merging and sorting) still work with such BAM records; tools that read
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	650 CIGAR will effectively ignore these records. It has been decided that future
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	651 tools will seamlessly recognize long-cigar records generated by option `-L`.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	652
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	653 TD;DR: if you work with ultra-long reads and use tools that only
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	654 process BAM files, please add option ``-L``.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	655
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	656 The cs optional tag
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	657 ^^^^^^^^^^^^^^^^^^^
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	658
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	659 The ``cs`` SAM/PAF tag encodes bases at mismatches and INDELs. It
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	660 matches regular expression
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	661 ``/(:[0-9]+\|\*[a-z][a-z]\|[=\+\-][A-Za-z]+)+/``. Like CIGAR, ``cs``
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	662 consists of series of operations. Each leading character specifies the
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	663 operation; the following sequence is the one involved in the operation.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	664
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	665 The ``cs`` tag is enabled by command line option ``--cs``. The following
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	666 alignment, for example:
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	667
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	668 .. code::
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	669
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	670 CGATCGATAAATAGAGTAG---GAATAGCA
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	671 \|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	672 CGATCG---AATAGAGTAGGTCGAATtGCA
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	673
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	674 is represented as ``:6-ata:10+gtc:4*at:3``, where ``:[0-9]+`` represents
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	675 an identical block, ``-ata`` represents a deltion, ``+gtc`` an insertion
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	676 and ``*at`` indicates reference base ``a`` is substituted with a query
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	677 base ``t``. It is similar to the ``MD`` SAM tag but is standalone and
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	678 easier to parse.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	679
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	680 If ``--cs=long`` is used, the ``cs`` string also contains identical
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	681 sequences in the alignment. The above example will become
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	682 ``=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA``. The long form of ``cs``
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	683 encodes both reference and query sequences in one string.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	684
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	685 Benchmarking
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	686 ~~~~~~~~~~~~
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	687
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	688 When comparing Winnowmap (v1.0) to minimap2 (v2.17-r954), we observed
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	689 a reduction in the mapping error-rate from 0.14% to 0.06% in the recently
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	690 finished human X chromosome, and from 3.6% to 0% within the highly repetitive
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	691 X centromere (3.1 Mbp). Winnowmap improves mapping accuracy within repeats
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	692 and achieves these results with sparser sampling, leading to better index
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	693 compression and competitive runtimes. By avoiding masking, we show that
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	694 Winnowmap maintains uniform minimizer density.
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	695
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	696 </help>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	697 <expand macro="citations"/>
1c070debf549 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f3c75fcbec417c749fca98a8d0cb3415c427dbb8" iuc parents: diff changeset	698 </tool>

Mercurial > repos > iuc > winnowmap

annotate winnowmap.xml @ 1:44231ef8167a draft