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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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 &#39;-O + -E*k&#39;. 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>