Mercurial > repos > iuc > quickmerge

annotate quickmerge.xml @ 1:d6d80fcb2168 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
author iuc
date Thu, 03 Oct 2024 14:28:22 +0000
parents 53920f3f0f1b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
1 <tool
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
2 id="quickmerge"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
3 name="QuickMerge"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
5 profile="21.05"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
6 >
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
7 <description>merge long-read and hybrid genome assemblies to increase contiguity</description>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
8
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
9 <macros>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
10 <token name="@TOOL_VERSION@">0.3</token>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
11 <token name="@VERSION_SUFFIX@">0</token>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
12 </macros>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
13
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
14 <xrefs>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
15 <xref type="bio.tools">quickmerge</xref>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
16 </xrefs>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
17
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
18 <requirements>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
19 <requirement type="package" version="@TOOL_VERSION@">quickmerge</requirement>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
20 <requirement type="package" version="0.1.4">fastkit</requirement>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
21 </requirements>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
22
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
23 <command detect_errors="exit_code"><![CDATA[
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
24
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
25 ## Strip spaces from FASTA header
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
26 fastkit format --strip-header-space '$input_ref' > input.ref.fasta
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
27 && fastkit format --strip-header-space '$input_query' > input.query.fasta
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
28
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
29 ## Nucmer step
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
30 ## ----------------------------------------------------------------------------
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
31
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
32 && nucmer
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
33 $advanced.nucmer_match_protocol
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
34 -l $advanced.nucmer_min_len
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
35 input.ref.fasta
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
36 input.query.fasta
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
37
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
38
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
39 ## Delta-filter step
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
40 ## ----------------------------------------------------------------------------
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
41
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
42 && delta-filter
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
43 $advanced.delta_map_ref
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
44 $advanced.delta_map_query
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
45 -l $advanced.delta_min_len
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
46
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
47 out.delta > out.rq.delta
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
48
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
49
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
50 ## Quickmerge step
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
51 ## ----------------------------------------------------------------------------
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
52
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
53 && quickmerge
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
54 -d out.rq.delta
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
55 -q input.query.fasta
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
56 -r input.ref.fasta
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
57 -p out
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
58 -hco $advanced.hco
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
59 -c $advanced.c
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
60 -l $advanced.l
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
61 -ml $advanced.ml
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
62
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
63 ]]></command>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
64
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
65 <inputs>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
66 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
67 name="input_query"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
68 type="data"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
69 format="fasta,fasta.gz"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
70 label="Query (hybrid) assembly"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
71 help="A hydrid or long-read assembly."
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
72 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
73 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
74 name="input_ref"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
75 type="data"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
76 format="fasta,fasta.gz"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
77 label="Reference assembly"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
78 help="The self assembly - this can also be a long-read assembly."
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
79 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
80
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
81 <section name="advanced" title="Advanced parameters" expanded="false">
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
82 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
83 name="nucmer_match_protocol"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
84 type="select"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
85 display="radio"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
86 label="Anchor matching protocol"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
87 help="By default, nucmer will include anchor matches that are unique
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
88 in the reference but not necessarily unique in the query. You can
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
89 change the protocol to include all matches, or only those unique to
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
90 both the reference and query sequence."
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
91 >
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
92 <option value="" selected="true">
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
93 Default (unique in reference only)
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
94 </option>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
95 <option value="--mum">
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
96 Include matches that are unique to both reference and query
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
97 </option>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
98 <option value="--maxmatch">
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
99 Include all matches
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
100 </option>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
101 </param>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
102
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
103 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
104 name="nucmer_min_len"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
105 type="integer"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
106 label="Nucmer -l"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
107 help="Minimum length for a single match (nt)"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
108 value="20"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
109 min="0"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
110 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
111
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
112 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
113 name="delta_min_len"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
114 type="integer"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
115 label="Delta-filter -l"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
116 help="Minimum alignment length (nt)"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
117 value="0"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
118 min="0"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
119 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
120
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
121 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
122 name="delta_map_ref"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
123 type="boolean"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
124 truevalue="-r"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
125 falsevalue=""
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
126 checked="true"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
127 label="Delta-filter -r"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
128 help="Maps each position of each reference to its best hit in the
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
129 query, allowing for query overlaps."
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
130 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
131
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
132 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
133 name="delta_map_query"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
134 type="boolean"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
135 truevalue="-q"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
136 falsevalue=""
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
137 checked="true"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
138 label="Delta-filter -q"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
139 help="Maps each position of each query to its best hit in the
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
140 reference, allowing for reference overlaps."
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
141 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
142
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
143 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
144 type="integer"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
145 argument="-l"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
146 help="Minimum seed contig length to be merged (nt). A good rule of
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
147 thumb is to start with the N50 of the self assembly."
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
148 value="0"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
149 min="0"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
150 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
151
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
152 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
153 type="integer"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
154 argument="-ml"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
155 help="Set the merging length cutoff (nt). This is especially helpful
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
156 for repeat-rich genomes, where a higher minimum length can reduce
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
157 errors arising from long repeats."
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
158 value="5000"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
159 min="0"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
160 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
161
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
162 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
163 type="float"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
164 argument="-hco"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
165 help="Controls the overlap cutoff used in selection of anchor contigs.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
166 Increasing this will raise stringency, resulting in fewer joins but
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
167 higher confidence."
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
168 value="5.0"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
169 min="0.0"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
170 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
171
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
172 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
173 type="float"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
174 argument="-c"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
175 help="Controls the overlap cutoff for contigs used for extension of
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
176 the anchor contig. Increasing this will raise stringency,
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
177 resulting in fewer joins but higher confidence."
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
178 value="1.5"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
179 min="0.0"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
180 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
181 </section>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
182
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
183 <section name="output" title="Optional outputs" expanded="true">
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
184 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
185 name="check_align_summary"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
186 type="boolean"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
187 label="Alignment summary table"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
188 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
189 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
190 name="check_anchor_summary"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
191 type="boolean"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
192 label="Anchor summary table"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
193 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
194 <param
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
195 name="check_param_summary"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
196 type="boolean"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
197 label="Parameter summary table"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
198 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
199 </section>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
200 </inputs>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
201
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
202 <outputs>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
203 <data
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
204 name="merged_fasta"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
205 format="fasta"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
206 from_work_dir="merged_out.fasta"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
207 label="${tool.name} on ${on_string}: Merged assembly"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
208 />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
209
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
210 <data
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
211 name="align_summary"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
212 format="tabular"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
213 from_work_dir="aln_summary_out.tsv"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
214 label="${tool.name} on ${on_string}: Alignment summary"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
215 >
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
216 <filter>output['check_align_summary']</filter>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
217 </data>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
218
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
219 <data
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
220 name="anchor_summary"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
221 format="tabular"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
222 from_work_dir="anchor_summary_out.txt"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
223 label="${tool.name} on ${on_string}: Anchor summary"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
224 >
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
225 <filter>output['check_anchor_summary']</filter>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
226 </data>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
227
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
228 <data
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
229 name="param_summary"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
230 format="tabular"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
231 from_work_dir="param_summary_out.txt"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
232 label="${tool.name} on ${on_string}: Parameter summary"
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
233 >
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
234 <filter>output['check_param_summary']</filter>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
235 </data>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
236 </outputs>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
237
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
238 <tests>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
239 <!-- Standard run -->
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
240 <test expect_num_outputs="1">
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
241 <param name="input_query" value="ecoli_nanopore.fasta" ftype="fasta" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
242 <param name="input_ref" value="ecoli_illumina.fasta" ftype="fasta" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
243 <output name="merged_fasta" ftype="fasta" file="merged.fasta" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
244 </test>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
245
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
246 <!-- Standard run with additional outputs -->
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
247 <test expect_num_outputs="4">
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
248 <param name="input_query" value="ecoli_nanopore.fasta" ftype="fasta" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
249 <param name="input_ref" value="ecoli_illumina.fasta" ftype="fasta" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
250 <param name="check_align_summary" value="true" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
251 <param name="check_anchor_summary" value="true" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
252 <param name="check_param_summary" value="true" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
253 <output name="merged_fasta" ftype="fasta" file="merged.fasta" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
254 <output name="align_summary" ftype="tabular" file="2_aln_summary_out.tsv" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
255 <output name="anchor_summary" ftype="tabular" file="2_anchor_summary_out.txt" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
256 <output name="param_summary" ftype="tabular" file="2_param_summary_out.txt" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
257 </test>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
258
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
259 <!-- Standard run with advanced params set -->
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
260 <test expect_num_outputs="1">
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
261 <param name="input_query" value="ecoli_nanopore.fasta" ftype="fasta" />
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
262 <param name="input_ref" value="ecoli_illumina.fasta" ftype="fasta" />
1
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
263 <section name="advanced">
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
264 <param name="nucmer_min_len" value="21" />
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
265 <param name="delta_min_len" value="1" />
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
266 <param name="hco" value="0" />
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
267 <param name="l" value="150" />
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
268 <param name="ml" value="4999" />
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
269 <param name="c" value="1.6" />
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
270 </section>
0
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
271 <output name="merged_fasta" ftype="fasta" file="merged.fasta" />
1
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
272 <assert_command>
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
273 <has_text text="-hco 0"/>
d6d80fcb2168 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit 6c59f5f3a581794eee2b28eaf4b091cc8ac8571e
iuc
parents: 0
diff changeset
274 </assert_command>
0
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
275 </test>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
276 </tests>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
277
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
278 <help><![CDATA[
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
279
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
280 .. class:: infomark
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
281
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
282 **What it does**
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
283
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
284 The program uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. This can be useful when long read coverage is limiting. For more details, please see the paper: (`10.1093/nar/gkw654 <https://doi.org/10.1093/nar/gkw654>`_) that describes it.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
285
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
286 Although this program was written to merge a hybrid assembly (e.g. as generated by DBG2OLC) and a PacBio or ONP only assembly, it can also be used to merge two different long molecule only assemblies (e.g. one generated with PBcR or canu and another generated with FALCON).
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
287
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
288 Please consult the `QuickMerge Wiki <https://github.com/mahulchak/quickmerge/wiki>`_ for extended usage information.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
289
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
290 **Why use quickmerge?**
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
291
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
292 - More bang for your buck by using complementary information from different assemblers.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
293 - It is fast. Takes less than a minute to run on most genomes. You run nucmer once (nucmer is the most time consuming step) and then you can run quickmerge over a large number of parameters in a very short time.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
294 - Requires only FASTA files and does not depend on any special data or computational resources.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
295 - Saves money. When long read coverage is limiting, there are some hybrid approaches that lead to good results (e.g. DBG2OLC). So quickmerge allows you to cut your long molecule requirement by as much as half by replacing the same with Illumina short reads. E.g. if you think you would get a N50 of 8Mb from 75X long reads (ONP or PacBio), try sequencing 45X long and 70X Illumina reads instead of 75X long reads. You may not need that extra 35X long reads.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
296 - Allows dramatic improvements with reanalysis of legacy data collected when long reads were prohibitively expensive. See an excellent example from `this paper by Thomas Mather <https://academic.oup.com/g3journal/article/10/3/899/6026189>`_ on the Soybean Aphid genome.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
297
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
298
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
299 **The process**
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
300
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
301 - **Nucmer** aligns the two assemblies so that the merger can find the correct splice sites
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
302 - **Delta-filter** filters out alignments with repeats and duplicates
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
303 - **Quickmerge** merges the aligned assemblies
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
304
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
305 **Inputs**
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
306
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
307 - **Query assembly**: a hydrid or long-read assembly (see `QuickMerge Wiki <https://github.com/mahulchak/quickmerge/wiki>`_ for more details)
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
308
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
309 - **Reference assembly**: "Self" assembly. Can also be a hybrid assembly
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
310
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
311 - **Nucmer -l**: the minimum length of a single match
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
312
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
313 - **Delta-filter -l**: the minimum length of a single alignment
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
314
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
315 - **hco**: controls the overlap cutoff used in selection of anchor contigs (default 5.0)
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
316
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
317 - **c**: controls the overlap cutoff for contigs used for extension of the anchor contig (default 1.5)
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
318
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
319 - **l**: controls the length cutoff for anchor contigs. A good rule of thumb is to start with the N50 of the self assembly. E.g. if the N50 of your self assembly is 2Mb then use 2000000 as your cutoff. Lowering this value may lead to more merging but may increase the probability of mis-joins.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
320
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
321 - **ml**: controls the minimum alignment length to be considered for merging. This is especially helpful for repeat-rich genomes (default 5000; higher recommended).
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
322
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
323 For both ``hco`` and ``c``, bigger the number, more stringent is the criteria for contig selection (which will lead to fewer contigs being merged). If they are too small (<1), chances of spurious merging will increase. It is better to be conservative while merging contigs!
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
324
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
325
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
326 **Outputs**
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
327
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
328 - **Merged assembly**: your merged assembly in FASTA format
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
329
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
330 - **Alignment summary**: tabular summary of alignments used for merging
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
331
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
332 - **Anchor summary**: tabular summary of anchor matches used for merging
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
333
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
334 - **Parameter summary**: summary of merge parameters
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
335
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
336
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
337 **Helpful tips**
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
338
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
339 - For optimal merging results, identify the major misassemblies (especially translocations and inversions) in the component assemblies and break the contigs at such misassembly boundaries. Alignment of the component assemblies to the merged assembly may help to identify such assembly errors because a specific error typically occurs in only one of the assemblies.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
340
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
341 - The FASTA sequence headers *should not have white spaces* in them. In case they do, as might happen for assemblies obtained from FALCON assembler, the white space needs to be removed before running.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
342
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
343 - You can run Ka-kit's `finisherSC <https://github.com/kakitone/finishingTool>`_ after running quickmerge to improve the contiguity even further.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
344
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
345 - Assembly polishing with Quiver and pilon before and after assembly merging is strongly recommended. However, if you are running finisherSC, you may perform the quiver polishing after the finisher step.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
346
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
347 - Check the merged assembly by aligning the hybrid and/or non-hybrid assembly to the merged assembly. You can use ``nucmer`` for alignment (with default anchoring) and ``mummerplot`` for dot plot visualization.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
348
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
349
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
350 Quickmerge was wrapped by the Galaxy Australia team.
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
351
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
352 ]]></help>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
353 <citations>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
354 <citation type="doi">https://doi.org/10.1093/nar/gkw654</citation>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
355 </citations>
53920f3f0f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge commit c171c7bde4063ec25fff4a284f5d0330d46ca290
iuc
parents:
diff changeset
356 </tool>