Mercurial > repos > abossers > mummer_toolsuite

annotate MUMmer/mummer_maxmatch.xml @ 0:59f302448cf6

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author abossers
date Tue, 07 Jun 2011 17:22:27 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
1 <tool id="mummer_maxmatch" name="MUMmer MaxMatch" version="0.9.alx" force_history_refresh="True">
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
2 <description>: Maximal exact sequence matching</description>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
3 <command>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
4 <!-- update this path to the installed location -->
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
5 /opt/MUMmer/MUMmer/$tool.cmd
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
6 #if $tool.cmd=="mummer":
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
7 $tool.cmd_extra
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
8 $tool.mum_ref_in
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
9 $tool.mum_q_in
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
10 #end if
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
11 #if $tool.cmd=="repeat-match":
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
12 -n $tool.rm_n
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
13 #if $tool.rm_E=="yes":
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
14 -E
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
15 #end if
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
16 $tool.cmd_extra
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
17 $tool.in_seq
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
18 #end if
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
19 #if $tool.cmd=="exact-tandems":
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
20 $tool.in_seq
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
21 $tool.et_minl
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
22 #end if
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
23 <!-- unfortunate somehow error state gets set also on succesfull jobs. Pipe io stderr to dev/null -->
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
24 2&gt;&amp;-
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
25 > $out_tool
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
26
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
27 </command>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
28 <inputs>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
29 <conditional name="tool">
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
30 <param name="cmd" type="select" value="mummer" label="MUMmer maximal matching" help="Algorithms are run with default parameters (none). For specific args see help below" >
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
31 <option value="mummer">mummer</option>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
32 <option value="repeat-match">repeat-match</option>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
33 <option value="exact-tandems">exact-tandems</option>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
34 </param>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
35 <when value="mummer">
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
36 <param name="mum_ref_in" type="data" format="fasta" label="Reference FastA file" />
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
37 <param name="mum_q_in" type="data" format="fasta" label="Query (multi) FastA sequence" />
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
38 <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="See specific cmd line options below for each tool" />
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
39 </when>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
40 <when value="repeat-match">
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
41 <param name="in_seq" type="data" format="fasta" label="FastA sequence file" />
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
42 <param name="rm_n" type="text" size="5" value="20" label="Minimum exact match length [-n]" />
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
43 <param name="rm_E" type="select" value="no" label="Use exhaustive (slow) search to find matches [-E]" >
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
44 <option value="no">No</option>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
45 <option value="yes">Yes</option>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
46 </param>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
47 <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="-n and -E are configured above. More specific cmd line options in help below." />
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
48 </when>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
49 <when value="exact-tandems">
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
50 <param name="in_seq" type="data" format="fasta" label="FastA sequence file" />
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
51 <param name="et_minl" type="text" size="5" value="20" label="Minimum length" />
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
52 </when>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
53 </conditional>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
54 </inputs>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
55 <outputs>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
56 <data name="out_tool" format="text" label="Max exact match output" />
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
57 </outputs>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
58 <requirements>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
59 <requirement type="binary">mummer</requirement>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
60 <requirement type="binary">repeat-match</requirement>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
61 <requirement type="binary">exact-tandems</requirement>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
62 </requirements>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
63 <tests>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
64 <test>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
65 </test>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
66 </tests>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
67 <help>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
68 |
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
69
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
70
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
71 **Reference**
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
72 =============
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
73
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
74 - **MUMmer MaxExactMatch Galaxy tool wrapper:** Alex Bossers, CVI of Wageningen UR, The Netherlands.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
75
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
76 - **MUMmer suite v3.22:** http://mummer.sourceforge.net
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
77
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
78 - **MUMmer tutorials:** http://mummer.sourceforge.net/examples/
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
79
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
80 Please do not use any of the command line options that modify prefixes or file names. As obvious
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
81 they are quite useless within galaxy and are likely to fail the routine!
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
82
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
83 If you found these tools/wrappers usefull in your research, please acknowledge our work. If you improve
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
84 or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
85
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
86
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
87
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
88 **MUMmer Maximal exact matching**
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
89 =================================
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
90
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
91 The heart of the MUMmer package is its suffix tree based maximal matching routines. These can be
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
92 used for repeat detection within a single sequence as is done by *repeat-match* and *exact-tandems*,
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
93 or can be used for the alignment of two or more sequences as is done by *mummer*.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
94
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
95 Mummer
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
96 ------
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
97
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
98 mummer is a suffix tree algorithm designed to find maximal exact matches of some minimum length
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
99 between two input sequences. by default mummer will only find maximal matches that are unique in
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
100 the entire set of reference sequences. The match lists produced by mummer can be used alone to
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
101 generate alignment dot plots, or can be passed on to the clustering algorithms for the identification
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
102 of longer non-exact regions of conservation. These match lists have great versatility because they
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
103 contain huge amounts of information and can be passed forward to other interpretation programs for
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
104 clustering, analysis, searching, etc.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
105
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
106
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
107 Repeat-match
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
108 ------------
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
109
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
110 repeat-match is a suffix tree algorithm designed to find maximal exact repeats within a single input
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
111 sequence. It uses a similar algorithm to mummer, but altered slightly to find maximal exact matches
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
112 within a single sequence.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
113
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
114 Output formatting varies depending on the command line parameters and the output can be quite large.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
115 The standard output format that results from running repeat-match with default parameters is as follows:
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
116 ::
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
117
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
118 Long Exact Matches:
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
119 Start1 Start2 Length
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
120 4919485 4919506r 22
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
121
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
122 The three columns are the first position of the repeat, the second position of the repeat, and the
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
123 length of the repeat respectively. Reverse complement repeat positions are denoted by an 'r'
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
124 following the Start2 position, and are relative to the forward strand of the sequence.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
125
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
126
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
127 Exact-tandems
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
128 -------------
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
129
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
130 exact-tandems is a wrapper script for the repeat-match program. It provides a list of exact tandem
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
131 repeats within a single input sequence. As with repeat-match the sequence file should contain only
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
132 one sequence in FastA format, however if multiple sequences exist the first one will be used. The
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
133 sequence may contain any set of upper and lowercase characters, thus DNA and protein sequence are
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
134 both allowed and matching is case insensitive. The minimum match length parameter should be a
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
135 positive integer, this value will be passed to the repeat-match program via the -n option.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
136
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
137 The output format of exact-tandems is as follows:
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
138 ::
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
139
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
140 Finding matches
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
141 Tandem repeats
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
142 Start Extent UnitLen Copies
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
143 416173 150 45 3.3
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
144
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
145 The four columns are the first position of the tandem, the extent of the repeat region, the length
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
146 of each tandem repeat unit, and the number of repeat units respectively.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
147
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
148
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
149
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
150 **Manuals and CMD line options (specific for each tool!):**
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
151 ===========================================================
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
152
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
153 **Mummer**
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
154
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
155 http://mummer.sourceforge.net/manual/#mummer
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
156
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
157 **Repeat-match**
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
158
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
159 http://mummer.sourceforge.net/manual/#repeat
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
160
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
161 **exact-tandems**
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
162
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
163 http://mummer.sourceforge.net/manual/#exact
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
164
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
165 |
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
166 |
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
167
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
168 </help>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
169 </tool>
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
170