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comparison MUMmer/mummer_utilities_tool.xml @ 0:59f302448cf6

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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
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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 /opt/MUMmer/MUMmer/$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="binary">mummer-tiling</requirement>
42 <requirement type="binary">mummer-snps</requirement>
43 <requirement type="binary">mummer-diff</requirement>
44 <requirement type="binary">mummer-coords</requirement>
45 <requirement type="binary">mummer-aligns</requirement>
46 <requirement type="binary">delta-filter</requirement>
47 </requirements>
48 <tests>
49 <test>
50 </test>
51 </tests>
52 <help>
53 |
54
55
56 **Reference**
57 =============
58
59 - **MUMmer_utilities Galaxy tool wrapper:** Alex Bossers, CVI of Wageningen UR, The Netherlands.
60
61 - **MUMmer utilities running on MUMmer delta file:** http://mummer.sourceforge.net/manual
62
63 - **MUMmer tutorials:** http://mummer.sourceforge.net/examples/
64
65 If you found these tools/wrappers usefull in your research, please acknowledge our work. If you improve
66 or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
67
68
69 **MUMmer Utilities**
70 ====================
71
72 All tools are using the MUMmer generated DELTA file! Additional arguments are only required for show-aligns.
73
74 Show-coords
75 -----------
76
77 show-coords parses the delta alignment output of NUCmer and PROmer, and displays summary
78 information such as position, percent identity and so on, of each alignment. It is the most
79 commonly used tool for analyzing the delta files. *Usually the -r is used to sort lines by reference*
80
81
82 Show-tiling
83 -----------
84
85 show-tiling attempts to construct a tiling path out of the query contigs as mapped to the reference
86 sequences. Given the delta alignment information of a few long reference sequences and many small
87 query contigs, show-tiling will determine the best mapped location of each query contig. Note that
88 each contig may only be tiled once, so repetitive regions may cause this program some difficulty.
89 This program is useful for aiding in the scaffolding and closure of an unfinished set of contigs,
90 if a suitable, high similarity reference genome is available. Or, if using PROmer, show-tiling will
91 help in the identification of syntenic regions and their contig's mapping to the references.
92
93 This program is not suitable for "many vs. many" assembly comparisons, however a new tool based on
94 the concepts of show-tiling should be available in the near future that will facilitate the mapping
95 of assembly contigs.
96
97
98 Show-snps
99 ---------
100
101 show-snps is a utility program for reporting polymorphisms contained in a delta encoded alignment
102 file output by NUCmer or PROmer. It catalogs all of the single nucleotide polymorphisms (SNPs) and
103 insertions/deletions within the delta file alignments. Polymorphisms are reported one per line, in
104 a delimited fashion similar to show-coords. Pairing this program with the appropriate MUMmer tools
105 can create an easy to use SNP pipeline for the rapid identification of putative SNPs between any
106 two sequence sets, as demonstrated in the manual SNP detection section.
107
108
109 Show-diff
110 ---------
111
112 Outputs a list of structural differences for each sequence in
113 the reference and query, sorted by position. For a reference
114 sequence R, and its matching query sequence Q, differences are
115 categorized as GAP (gap between two mutually consistent alignments),
116 DUP (inserted duplication), BRK (other inserted sequence), JMP
117 (rearrangement), INV (rearrangement with inversion), SEQ
118 (rearrangement with another sequence). The first five columns of
119 the output are seq ID, feature type, feature start, feature end,
120 and feature length. Additional columns are added depending on the
121 feature type. Negative feature lengths indicate overlapping adjacent
122 alignment blocks.
123 ::
124
125 IDR GAP gap-start gap-end gap-length-R gap-length-Q gap-diff
126 IDR DUP dup-start dup-end dup-length
127 IDR BRK gap-start gap-end gap-length
128 IDR JMP gap-start gap-end gap-length
129 IDR INV gap-start gap-end gap-length
130 IDR SEQ gap-start gap-end gap-length prev-sequence next-sequence
131
132 Positions always reference the sequence with the given ID. The
133 sum of the fifth column (ignoring negative values) is the total
134 amount of inserted sequence. Summing the fifth column after removing
135 DUP features is total unique inserted sequence. Note that unaligned
136 sequence are not counted, and could represent additional "unique"
137 sequences. See documentation for tips on how to interpret these
138 alignment break features.
139
140
141 Show-aligns
142 -----------
143
144 show-aligns parses the delta encoded alignment output of NUCmer and PROmer, and displays
145 the pair-wise alignments from the two sequences specified on the command line. It is handy
146 for identifying the exact location of errors and looking for SNPs between two sequences.
147
148
149 Delta-filter
150 ------------
151
152 delta-filter is a utility program for the manipulation of the delta encoded alignment files output
153 by the NUCmer and PROmer pipelines. It takes a delta file as input and filters the information based
154 on the various command line switches, outputting only the desired alignments to stdout. Options to filter by
155 alignment length, identity, uniqueness and consistency are provided. Certain combinations of these
156 options can greatly reduce the number of unwanted alignments in the delta file, thus making the output
157 of programs such as show-coords more comprehendible.
158
159
160
161 **CMD line options (specific for each tool!):**
162 ===============================================
163
164 **Show-coords**
165
166 http://mummer.sourceforge.net/manual/#coords
167
168 **Show-tiling**
169
170 http://mummer.sourceforge.net/manual/#tiling
171
172 **Show-snps**
173
174 http://mummer.sourceforge.net/manual/#snps
175
176 **Show-aligns**
177
178 http://mummer.sourceforge.net/manual/#aligns
179
180 **Delta-filter**
181
182 http://mummer.sourceforge.net/manual/#filter
183
184
185 </help>
186 </tool>
187