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1 <tool id="patser-v3e" name="patser" description="finds putative transcription factor binding sites" version="0.1.2">
2 <requirements>
3 <requirement type="package" version="v3e">patser</requirement>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8
9 <command><![CDATA[
10 ## We need to transform the fasta input file into the awkward format in that patser can work on
11 ## The fasta header must be followed by the nucleotide sequence encapsulated by backslashes.
12 ## We simply add backslashes before and after each fasta header and skip the first line,
13 ## and we add a final backslash at the end of the file.
14 awk '/>/{print "\\"}1' "$input_fasta"|awk '/>/{print;print "\\";next}1'|tail -n +2 >> special.fa;
15 echo "\\" >> special.fa;
16 patser-v3e -A a:t "$at" c:g "$gc" -m "$input_matrix" -b "$b" $c -d1 -ls "$ls" -f special.fa "$p" > "$output1"
17 ]]></command>
18 <inputs>
19 <param type="data" name="input_matrix" format="txt" help="Provide alignment matrix file"/>
20 <param type="data" name="input_fasta" format="fasta" help="Fasta file with sequence"/>
21 <param name="v" type="boolean" label="the matrix is a vertical matrix (default: horizontal matrix)"
22 truevalue="-v" falsevalue=""
23 help="commandline option -v" />
24 <param name="b" type="integer" label="Correction added to the elements of the alignment matrix"
25 value="1"
26 help="commandline option -b" />
27 <param name="gc" type="float" label="Enter the GC frequency"
28 value="0.25" min="0" max="1"
29 help="commandline option -A gc:(value)" />
30 <param name="at" type="float" label="Enter the AT frequency"
31 value="0.25" min="0" max="1"
32 help="commandline option -A at:" />
33 <param name="c" type="boolean" label="Also score the complementary sequences"
34 truevalue="-c" falsevalue="" checked="true"
35 help="commandline option -c: Also score the complementary sequences. The complements are determined by the program and are not explicitly stated in the sequence fasta" />
36 <param name="p" type="boolean" label="print the weight matrix derived from the alignment matrix"
37 truevalue="-p" falsevalue="" checked="true"
38 help="commandline option -p" />
39 <param name="ls" type="float" label="Lower-threshold score, inclusive"
40 value="7"
41 help="commandline option -ls" />
42 </inputs>
43 <outputs>
44 <data name="output1" format="txt" from_work_dir="output.txt" />
45 </outputs>
46 <tests>
47 <test>
48 <param name="input_matrix" value="PWM_training_EcR-USP.txt"/>
49 <param name="input_fasta" value="EcR_USP_224.fa"/>
50 <output name="output1" file="output.txt" lines_diff="6"/>
51 </test>
52 </tests>
53 <help><![CDATA[
54
55 This wrapper has been written by Marius van den Beek (m.vandenbeek at gmail.com).
56 Patser is available from http://stormo.wustl.edu/resources.html .
57
58 -------------------------------------------------------------------------------
59
60 The following options can be determined on the command line:
61
62 ::
63
64 0) -h: print these directions.
65
66 1) Matrix options.
67 -m filename: (default name is "matrix") file containing the matrix.
68 -w: the matrix is a weight matrix (default: alignment matrix)
69 -b number: a non-negative number indicating the total number of
70 pseudo-counts added to each alignment position (default: 1).
71 Before converting an alignment matrix to a weight matrix, the
72 total pseudo-counts multiplied by the a priori probability
73 (see section 3 below) of the corresponding letter is added
74 to each matrix element.
75 -v: the matrix is a vertical matrix (default: horizontal matrix).
76 -p: print the weight matrix derived from the alignment matrix.
77
78 2) -f filename: this file (default: read from the standard input) contains
79 the names of the sequences. The corresponding sequence may follow
80 its name if the sequence is enclosed between backslashes (\).
81 Otherwise, the sequence is assumed to be in a separate file having
82 the indicated name.
83
84 In the sequences, whitespace, slashes (/), periods, dashes (unless
85 part of an integer when the "-i" option is used), and comments
86 beginning with ';', '%', or '#' are ignored. When using letter
87 characters (i.e., with the "-a" or "-A" alphabet option), integers
88 are also ignored so that the sequence file can contain positional
89 information. When using integer characters (i.e., with the "-i"
90 alphabet option) the integers must be separated by whitespace.
91
92 A "-c" preceding the name of a sequence file indicates that the
93 corresponding sequence is circular.
94
95 3) Alphabet options---the three options in this section are mutually
96 exclusive (default: "-a alphabet"). The a priori probabilities mentioned
97 below are used when converting an alignment matrix to a weight matrix.
98 -a filename: file containing the alphabet and normalization information.
99
100 Each line contains a letter (a symbol in the alphabet) followed by an
101 optional normalization number (default: 1.0). The normalization is
102 based on the relative a priori probabilities of the letters. For
103 nucleic acids, this might be be the genomic frequency of the bases
104 or the frequencies observed in the data used to generate the alignment.
105 In nucleic acid alphabets, a letter and its complement appear on the
106 same line, separated by a colon (a letter can be its own complement,
107 e.g. when using a dimer alphabet). Complementary letters may use the
108 same normalization number. Only the standard 26 letters are
109 permissible; however, when the "-CS" option is used, the alphabet is
110 case sensitive so that a total of 52 different characters are possible.
111
112 POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS:
113 letter
114 letter normalization
115
116 POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS:
117 letter:complement
118 letter:complement normalization
119 letter:complement normalization:complement's_normalization
120
121 -i filename: same as the "-a" option, except that the symbols of
122 the alphabet are represented by integers rather than by letters.
123 Any integer permitted by the machine is a permissible symbol.
124
125 -A alphabet_and_normalization_information: same as "-a" option, except
126 information appears on the command line (e.g., -A a:t 3 c:g 2).
127
128 4) Alphabet modifiers indicating whether ascii alphabets are case
129 sensitive---the two options in this section are mutually exclusive
130 with each other and with the "-i" option (default: ascii alphabets are
131 case insensitive).
132 -CS: ascii alphabets are case sensitive.
133 -CM: ascii alphabets are case insensitive, but mark the location
134 of lowercase letters by printing a line containing their locations.
135 This option is useful when lowercase letters indicate a functional
136 landmark such as a transcriptional start in a DNA sequence.
137
138 5) Options for adjusting or restricting which information
139 and scores are printed.
140 The "-ls", "-li", and "-lp" options are mutually exclusive.
141 -c: also score the complementary sequences. The complements are
142 determined by the program and are not explicitly stated in the
143 sequence files.
144 -ls number: lower threshold for printing scores, inclusive
145 (formerly the -l option).
146 -li: assume that the maximum ln(p-value) for printing scores equals
147 the negative of the sample-size adjusted information content;
148 indirectly determines the lower threshold for printing scores.
149 -lp number: the maximum ln(p-value) for printing scores; indirectly
150 determines the lower threshold for printing scores.
151 -u number: upper threshold for printing scores, exclusive.
152
153 -t: just print the top score for each sequence.
154 -t number: print the indicated number of top scores for each sequence.
155 -ds: if the "-t number" option is used, print the top scores for each
156 sequence in the order of decreasing score (default: order the
157 scores according to their position within the sequence).
158 -e number: the small difference for considering 2 scores equal
159 (default: 0.000001)
160
161 -s: print the sequence corresponding to each score that is printed.
162
163 6) Options indicating how unrecognized symbols are treated (default: -d1).
164 Symbols are letters when option "-a" or "-A" is used;
165 symbols are integers when option "-i" is used.
166 The following three options are mutually exclusive.
167 -d0: treat unrecognized symbols as errors and exit the program.
168 -d1: treat unrecognized symbols as discontinuities, but print a warning.
169 Treating a symbol as a discontinuity means that any L-mer
170 containing the unrecognized symbol will be ignored.
171 -d2: treat unrecognized symbols as discontinuities, and print NO warning.
172
173 7) Options for adjusting the estimation of p-value.
174 If the -R option is set to zero, the p-value is not estimated.
175 -R number: the range for approximating a column of the weight matrix with
176 integers (default: 10000). This number is the difference
177 between the largest and smallest integers used to estimate
178 the scores. Higher values increase precision, but will take
179 longer to calculate the table of p-values.
180 -M number: the minimum score for approximating p-values (default: 0).
181 Higher values will increase precision,
182 but may miss interesting scores.
183
184
185 ::
186
187 ----------------------------------------------------------------------
188
189 Copyright 1990, 1994, 1995, 1996, 2000, 2001, 2002 Gerald Z. Hertz
190 May be copied for noncommercial purposes.
191
192 Author:
193 Gerald Z. Hertz
194 gzhertz AT alum.mit.edu
195
196 PATSER (version 3e)
197
198 This program scores the L-mers (subsequences of length L) of the
199 indicated sequences against the indicated alignment or weight matrix.
200 The elements of an alignment matrix are simply the number of times
201 that the indicated letter is observed at the indicated position of a
202 sequence alignment. Such elements must be processed before the matrix
203 can be used to score an L-mer (e.g., Hertz and Stormo, 1999,
204 Bioinformatics, 15:563-577). A weight matrix is a matrix whose
205 elements are in a form considered appropriate for scoring an L-mer.
206
207 Each element of an alignment matrix is converted to an element of a
208 weight matrix by first adding pseudo-counts in proportion to the a
209 priori probability of the corresponding letter (see option "-b" in
210 section 1 below) and dividing by the total number of sequences plus
211 the total number of pseudo-counts. The resulting frequency is
212 normalized by the a priori probability for the corresponding letter.
213 The final quotient is converted to an element of a weight matrix by
214 taking its natural logarithm. The use of pseudo-counts here differs
215 from previous versions of this program by being proportional to the a
216 priori probability.
217
218 Version 3 of this program differs from previous versions by also
219 numerically estimating the p-value of the scores. The p-value
220 calculated here is the probability of observing a particular score or
221 higher at a particular sequence position and does NOT account for the
222 total amount of sequence being scored. P-values are estimated by the
223 method described in Staden, 1989, CABIOS, p. 89--96. The relative
224 value for each element of the weight matrix is approximated by
225 integers in a range determined by the "-R" and "-M" options (section 6
226 below). The p-value is calculated for each possible integer score and
227 the values are stored. The actual scores for the sequences are
228 determined from the true weight matrix. The true scores are converted
229 to their corresponding integer values and their p-values are looked up.
230
231 Matrices can be either horizontal or vertical. In a horizontal
232 matrix, the columns correspond to the positions within the pattern,
233 and the rows correspond to the letters. Each row begins with the
234 corresponding letter (or integer, if the "-i" option is used). In a
235 vertical matrix, the rows correspond to the positions within the
236 pattern, and the columns correspond to the letters. The first row
237 contains the letters (or integers, if the "-i" option is used)
238 corresponding to each column. In both types of matrices, spaces,
239 tabs, and vertical bars (|) are ignored. The output of the "consensus"
240 and "wconsensus" programs consists of horizontal alignment matrices.
241
242 The input files can contain comments according to the following
243 convention. The portion of a line following a ';', '%', or '#' is
244 considered a comment and is ignored. Comments can begin anywhere in a
245 line and always end at the end of the line. The output of this
246 program is sent to the standard output.
247
248
249 ]]></help>
250 <citations>
251 <citation type="doi">10.1093/bioinformatics/15.7.563</citation>
252 </citations>
253 </tool>