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comparison MUMmer/mummer_utilities_tool.xml @ 2:479eb076cd23

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Add revised mummer toolshed files to testtoolshed
author abossers
date Tue, 28 Oct 2014 16:59:33 +0100
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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 $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