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Uploaded the config file
author malex
date Wed, 30 Nov 2011 12:18:10 -0500
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1 <tool id="trf" name="Tandem Repeats Finder" version="4.04">
2 <description>Detect tandem repeats that have undergone extensive mutational change</description>
3 <command interpreter="python">trf_wrapper.py
4 $input1 $match $mismatch $delta $mprobability $iprobability $minscore
5 $maxperiod $masked $flanking $noredundancy -o $outputdat -k $outputmask -t
6 $report -i $indices
7 </command>
8 <inputs>
9 <param format="fasta" name="input1" type="data">
10 <label>Sequence</label>
11 </param>
12 <param name="match" size="4" type="text" value="2">
13 <label>Match</label>
14 </param>
15 <param name="mismatch" size="4" type="text" value="7">
16 <label>Mismatch</label>
17 </param>
18 <param name="delta" size="4" type="text" value="7">
19 <label>Indels</label>
20 </param>
21 <param name="mprobability" size="4" type="integer" value="80" label="Matching probability, %">
22 <validator type="in_range" message="(10-100)" min="10" max="100"/>
23 </param>
24 <param name="iprobability" size="4" type="integer" value="10" label="Indel probability, %">
25 <validator type="in_range" message="(10-100)" min="10" max="100"/>
26 </param>
27 <param name="minscore" size="3" type="integer" value="50">
28 <label>Minimum alignment score for repeat reporting</label>
29 <validator type="in_range" message="(30-150)" min="30" max="150"/>
30 </param>
31 <param name="maxperiod" size="4" type="integer" value="500">
32 <label>Maximum period size for repeat reporting</label>
33 <validator type="in_range" message="(1-2000)" min="1" max="2000"/>
34 </param>
35 <param name="flanking" type="boolean" checked="no" truevalue="-f" falsevalue="" display="checkboxes">
36 <label>Flanking sequence</label>
37 </param>
38 <param name="masked" type="boolean" checked="no" truevalue="-m" falsevalue="" display="checkboxes">
39 <label>Masked Sequence File</label>
40 </param>
41 <param name="noredundancy" type="boolean" checked="no" truevalue="-r" falsevalue="" display="checkboxes">
42 <label>No redundancy elimination</label>
43 </param>
44 </inputs>
45 <outputs>
46 <data format="html" name="report" label="${tool.name} on ${on_string}: Report"/>
47 <data format="html" name="indices" label="${tool.name} on ${on_string}: Indices"/>
48 <data format="tabular" name="outputdat" label="${tool.name} on ${on_string}: Data"/>
49 <data format="txt" name="outputmask" label="${tool.name} on ${on_string}: Masked Sequence">
50 <filter>masked is True</filter>
51 </data>
52 </outputs>
53 <tests>
54 <test>
55 <param name="input1" value="trf_input.fasta"/>
56 <param name="match" value="2"/>
57 <param name="mismatch" value="7"/>
58 <param name="delta" value="7"/>
59 <param name="mprobability" value="80"/>
60 <param name="iprobability" value="10"/>
61 <param name="minscore" value="50"/>
62 <param name="maxperiod" value="500"/>
63 <param name="masked" value="-m"/>
64 <param name="flanking" value=""/>
65 <param name="noredundancy" value=""/>
66 <output name="outputdat" file="trf_out.dat"/>
67 <output name="outputmask" file="trf_out.mask"/>
68 </test>
69 </tests>
70 <help>
71 .. class:: warningmark
72
73 The input dataset needs to be in FASTA format.
74
75 -----
76
77 Tandem Repeats Finder, Version 4.04
78
79 Copyright (C) Dr. Gary Benson 1999-2004. All rights reserved.
80
81
82 Please cite:
83
84 G. Benson, "Tandem repeats finder: a program to analyze DNA sequences" Nucleic Acids Research (1999) Vol. 27, No. 2, pp. 573-580.
85
86
87 A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern
88 of nucleotides. Tandem Repeats Finder is a program to locate and display tandem
89 repeats in DNA sequences. In order to use the program, the user submits a
90 sequence in FASTA format. There is no need to specify the pattern, the size of
91 the pattern or any other parameter. The output consists of two files: a repeat
92 table file and an alignment file. The repeat table contains information about
93 each repeat, including its location, size, number of copies and nucleotide
94 content. Clicking on the location indices for one of the table entries opens a
95 second web browser that shows an alignment of the copies against a consensus
96 pattern. The program is very fast, analyzing sequences on the order of .5Mb in
97 just a few seconds. Submitted sequences may be of arbitrary length. Repeats
98 with pattern size in the range from 1 to 2000 bases are detected.
99 </help>
100 </tool>
101 <!--
102 Please use: trf File Match Mismatch Delta PM PI Minscore MaxPeriod [options]
103 Where: (all weights, penalties, and scores are positive)
104 File = sequences input file
105 Match = matching weight
106 Mismatch = mismatching penalty
107 Delta = indel penalty
108 PM = match probability (whole number)
109 PI = indel probability (whole number)
110 Minscore = minimum alignment score to report
111 MaxPeriod = maximum period size to report
112 [options] = one or more of the following :
113 -m masked sequence file
114 -f flanking sequence
115 -d data file
116 -h suppress html output
117 -r no redundancy elimination
118 Note the sequence file should be in FASTA format:
119 -->