|
0
|
1 <tool id="mummer_utilities_tool" name="MUMmer utilities" version="0.9.alx" force_history_refresh="True">
|
|
|
2 <description>: Show and filter on sequence delta file</description>
|
|
|
3 <command>
|
|
|
4 <!-- update this path to the installed location -->
|
|
|
5 $tool.cmd
|
|
|
6 $cmd_extra
|
|
|
7 $input_delta
|
|
|
8 #if $tool.cmd=="show-aligns":
|
|
|
9 $tool.aligns1
|
|
|
10 $tool.aligns2
|
|
|
11 #end if
|
|
|
12 > $out_tool
|
|
|
13 </command>
|
|
|
14 <inputs>
|
|
|
15 <conditional name="tool">
|
|
|
16 <param name="cmd" type="select" value="show-snps" label="MUMmer utility" help="Utilities are run with default parameters (none). For utility specific args see help below" >
|
|
|
17 <option value="show-snps">show SNPs</option>
|
|
|
18 <option value="show-tiling">show tiling</option>
|
|
|
19 <option value="show-diff">show diff</option>
|
|
|
20 <option value="show-coords">show coords</option>
|
|
|
21 <option value="show-aligns">show aligns</option>
|
|
|
22 <option value="delta-filter">delta filter</option>
|
|
|
23 </param>
|
|
|
24 <when value="show-aligns">
|
|
|
25 <param name="aligns1" type="text" size="40" value="" label="IdR" help="the FastA header tag of the desired reference sequence" />
|
|
|
26 <param name="aligns2" type="text" size="40" value="" label="IdQ" help="the FastA header tag of the desired query sequence" />
|
|
|
27 </when>
|
|
|
28 <when value="show-snps" />
|
|
|
29 <when value="show-tiling" />
|
|
|
30 <when value="show-coords" />
|
|
|
31 <when value="show-diff" />
|
|
|
32 <when value="delta-filter" />
|
|
|
33 </conditional>
|
|
|
34 <param name="input_delta" type="data" format="tabular" label="MUMmer delta file" />
|
|
|
35 <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="see specific cmd line options below for each tool" />
|
|
|
36 </inputs>
|
|
|
37 <outputs>
|
|
|
38 <data name="out_tool" format="text" />
|
|
|
39 </outputs>
|
|
|
40 <requirements>
|
|
|
41 <!-- <requirement type="set_environment" version="3.23">MUMMER_PATH</requirement> -->
|
|
|
42 <requirement type="package" version="4.6.4">gnuplot</requirement>
|
|
|
43 <requirement type="package" version="3.23">mummer</requirement>
|
|
|
44 </requirements>
|
|
|
45 <tests>
|
|
|
46 <test>
|
|
|
47 </test>
|
|
|
48 </tests>
|
|
|
49 <help>
|
|
|
50 |
|
|
|
51
|
|
|
52
|
|
|
53 **Reference**
|
|
|
54 =============
|
|
|
55
|
|
|
56 - **MUMmer_utilities Galaxy tool wrapper:** Alex Bossers, CVI of Wageningen UR, The Netherlands.
|
|
|
57
|
|
|
58 - **MUMmer utilities running on MUMmer delta file:** http://mummer.sourceforge.net/manual
|
|
|
59
|
|
|
60 - **MUMmer tutorials:** http://mummer.sourceforge.net/examples/
|
|
|
61
|
|
|
62 If you found these tools/wrappers usefull in your research, please acknowledge our work. If you improve
|
|
|
63 or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
|
|
|
64
|
|
|
65
|
|
|
66 **MUMmer Utilities**
|
|
|
67 ====================
|
|
|
68
|
|
|
69 All tools are using the MUMmer generated DELTA file! Additional arguments are only required for show-aligns.
|
|
|
70
|
|
|
71 Show-coords
|
|
|
72 -----------
|
|
|
73
|
|
|
74 show-coords parses the delta alignment output of NUCmer and PROmer, and displays summary
|
|
|
75 information such as position, percent identity and so on, of each alignment. It is the most
|
|
|
76 commonly used tool for analyzing the delta files. *Usually the -r is used to sort lines by reference*
|
|
|
77
|
|
|
78
|
|
|
79 Show-tiling
|
|
|
80 -----------
|
|
|
81
|
|
|
82 show-tiling attempts to construct a tiling path out of the query contigs as mapped to the reference
|
|
|
83 sequences. Given the delta alignment information of a few long reference sequences and many small
|
|
|
84 query contigs, show-tiling will determine the best mapped location of each query contig. Note that
|
|
|
85 each contig may only be tiled once, so repetitive regions may cause this program some difficulty.
|
|
|
86 This program is useful for aiding in the scaffolding and closure of an unfinished set of contigs,
|
|
|
87 if a suitable, high similarity reference genome is available. Or, if using PROmer, show-tiling will
|
|
|
88 help in the identification of syntenic regions and their contig's mapping to the references.
|
|
|
89
|
|
|
90 This program is not suitable for "many vs. many" assembly comparisons, however a new tool based on
|
|
|
91 the concepts of show-tiling should be available in the near future that will facilitate the mapping
|
|
|
92 of assembly contigs.
|
|
|
93
|
|
|
94
|
|
|
95 Show-snps
|
|
|
96 ---------
|
|
|
97
|
|
|
98 show-snps is a utility program for reporting polymorphisms contained in a delta encoded alignment
|
|
|
99 file output by NUCmer or PROmer. It catalogs all of the single nucleotide polymorphisms (SNPs) and
|
|
|
100 insertions/deletions within the delta file alignments. Polymorphisms are reported one per line, in
|
|
|
101 a delimited fashion similar to show-coords. Pairing this program with the appropriate MUMmer tools
|
|
|
102 can create an easy to use SNP pipeline for the rapid identification of putative SNPs between any
|
|
|
103 two sequence sets, as demonstrated in the manual SNP detection section.
|
|
|
104
|
|
|
105
|
|
|
106 Show-diff
|
|
|
107 ---------
|
|
|
108
|
|
|
109 Outputs a list of structural differences for each sequence in
|
|
|
110 the reference and query, sorted by position. For a reference
|
|
|
111 sequence R, and its matching query sequence Q, differences are
|
|
|
112 categorized as GAP (gap between two mutually consistent alignments),
|
|
|
113 DUP (inserted duplication), BRK (other inserted sequence), JMP
|
|
|
114 (rearrangement), INV (rearrangement with inversion), SEQ
|
|
|
115 (rearrangement with another sequence). The first five columns of
|
|
|
116 the output are seq ID, feature type, feature start, feature end,
|
|
|
117 and feature length. Additional columns are added depending on the
|
|
|
118 feature type. Negative feature lengths indicate overlapping adjacent
|
|
|
119 alignment blocks.
|
|
|
120 ::
|
|
|
121
|
|
|
122 IDR GAP gap-start gap-end gap-length-R gap-length-Q gap-diff
|
|
|
123 IDR DUP dup-start dup-end dup-length
|
|
|
124 IDR BRK gap-start gap-end gap-length
|
|
|
125 IDR JMP gap-start gap-end gap-length
|
|
|
126 IDR INV gap-start gap-end gap-length
|
|
|
127 IDR SEQ gap-start gap-end gap-length prev-sequence next-sequence
|
|
|
128
|
|
|
129 Positions always reference the sequence with the given ID. The
|
|
|
130 sum of the fifth column (ignoring negative values) is the total
|
|
|
131 amount of inserted sequence. Summing the fifth column after removing
|
|
|
132 DUP features is total unique inserted sequence. Note that unaligned
|
|
|
133 sequence are not counted, and could represent additional "unique"
|
|
|
134 sequences. See documentation for tips on how to interpret these
|
|
|
135 alignment break features.
|
|
|
136
|
|
|
137
|
|
|
138 Show-aligns
|
|
|
139 -----------
|
|
|
140
|
|
|
141 show-aligns parses the delta encoded alignment output of NUCmer and PROmer, and displays
|
|
|
142 the pair-wise alignments from the two sequences specified on the command line. It is handy
|
|
|
143 for identifying the exact location of errors and looking for SNPs between two sequences.
|
|
|
144
|
|
|
145
|
|
|
146 Delta-filter
|
|
|
147 ------------
|
|
|
148
|
|
|
149 delta-filter is a utility program for the manipulation of the delta encoded alignment files output
|
|
|
150 by the NUCmer and PROmer pipelines. It takes a delta file as input and filters the information based
|
|
|
151 on the various command line switches, outputting only the desired alignments to stdout. Options to filter by
|
|
|
152 alignment length, identity, uniqueness and consistency are provided. Certain combinations of these
|
|
|
153 options can greatly reduce the number of unwanted alignments in the delta file, thus making the output
|
|
|
154 of programs such as show-coords more comprehendible.
|
|
|
155
|
|
|
156
|
|
|
157
|
|
|
158 **CMD line options (specific for each tool!):**
|
|
|
159 ===============================================
|
|
|
160
|
|
|
161 **Show-coords**
|
|
|
162
|
|
|
163 http://mummer.sourceforge.net/manual/#coords
|
|
|
164
|
|
|
165 **Show-tiling**
|
|
|
166
|
|
|
167 http://mummer.sourceforge.net/manual/#tiling
|
|
|
168
|
|
|
169 **Show-snps**
|
|
|
170
|
|
|
171 http://mummer.sourceforge.net/manual/#snps
|
|
|
172
|
|
|
173 **Show-aligns**
|
|
|
174
|
|
|
175 http://mummer.sourceforge.net/manual/#aligns
|
|
|
176
|
|
|
177 **Delta-filter**
|
|
|
178
|
|
|
179 http://mummer.sourceforge.net/manual/#filter
|
|
|
180
|
|
|
181
|
|
|
182 </help>
|
|
|
183 </tool>
|
|
|
184
|
