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annotate patser-v3e.xml @ 1:4d9823e0f6f7 draft default tip
planemo upload for repository http://stormo.wustl.edu/resources.html
| author | mvdbeek |
|---|---|
| date | Mon, 29 Jun 2015 05:57:00 -0400 |
| parents | f9ab3aa3e538 |
| children |
| rev | line source |
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1
4d9823e0f6f7
planemo upload for repository http://stormo.wustl.edu/resources.html
mvdbeek
parents:
0
diff
changeset
|
1 <tool id="patser-v3e" name="patser" version="0.1.2"> |
|
4d9823e0f6f7
planemo upload for repository http://stormo.wustl.edu/resources.html
mvdbeek
parents:
0
diff
changeset
|
2 <description>finds putative transcription factor binding sites</description> |
| 0 | 3 <requirements> |
| 4 <requirement type="package" version="v3e">patser</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 | |
| 10 <command><![CDATA[ | |
| 11 ## We need to transform the fasta input file into the awkward format in that patser can work on | |
| 12 ## The fasta header must be followed by the nucleotide sequence encapsulated by backslashes. | |
| 13 ## We simply add backslashes before and after each fasta header and skip the first line, | |
| 14 ## and we add a final backslash at the end of the file. | |
| 15 awk '/>/{print "\\"}1' "$input_fasta"|awk '/>/{print;print "\\";next}1'|tail -n +2 >> special.fa; | |
| 16 echo "\\" >> special.fa; | |
| 17 patser-v3e -A a:t "$at" c:g "$gc" -m "$input_matrix" -b "$b" $c -d1 -ls "$ls" -f special.fa "$p" > "$output1" | |
| 18 ]]></command> | |
| 19 <inputs> | |
| 20 <param type="data" name="input_matrix" format="txt" help="Provide alignment matrix file"/> | |
| 21 <param type="data" name="input_fasta" format="fasta" help="Fasta file with sequence"/> | |
| 22 <param name="v" type="boolean" label="the matrix is a vertical matrix (default: horizontal matrix)" | |
| 23 truevalue="-v" falsevalue="" | |
| 24 help="commandline option -v" /> | |
| 25 <param name="b" type="integer" label="Correction added to the elements of the alignment matrix" | |
| 26 value="1" | |
| 27 help="commandline option -b" /> | |
| 28 <param name="gc" type="float" label="Enter the GC frequency" | |
| 29 value="0.25" min="0" max="1" | |
| 30 help="commandline option -A gc:(value)" /> | |
| 31 <param name="at" type="float" label="Enter the AT frequency" | |
| 32 value="0.25" min="0" max="1" | |
| 33 help="commandline option -A at:" /> | |
| 34 <param name="c" type="boolean" label="Also score the complementary sequences" | |
| 35 truevalue="-c" falsevalue="" checked="true" | |
| 36 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" /> | |
| 37 <param name="p" type="boolean" label="print the weight matrix derived from the alignment matrix" | |
| 38 truevalue="-p" falsevalue="" checked="true" | |
| 39 help="commandline option -p" /> | |
| 40 <param name="ls" type="float" label="Lower-threshold score, inclusive" | |
| 41 value="7" | |
| 42 help="commandline option -ls" /> | |
| 43 </inputs> | |
| 44 <outputs> | |
| 45 <data name="output1" format="txt" from_work_dir="output.txt" /> | |
| 46 </outputs> | |
| 47 <tests> | |
| 48 <test> | |
| 49 <param name="input_matrix" value="PWM_training_EcR-USP.txt"/> | |
| 50 <param name="input_fasta" value="EcR_USP_224.fa"/> | |
| 51 <output name="output1" file="output.txt" lines_diff="6"/> | |
| 52 </test> | |
| 53 </tests> | |
| 54 <help><![CDATA[ | |
| 55 | |
| 56 This wrapper has been written by Marius van den Beek (m.vandenbeek at gmail.com). | |
| 57 Patser is available from http://stormo.wustl.edu/resources.html . | |
| 58 | |
| 59 ------------------------------------------------------------------------------- | |
| 60 | |
| 61 The following options can be determined on the command line: | |
| 62 | |
| 63 :: | |
| 64 | |
| 65 0) -h: print these directions. | |
| 66 | |
| 67 1) Matrix options. | |
| 68 -m filename: (default name is "matrix") file containing the matrix. | |
| 69 -w: the matrix is a weight matrix (default: alignment matrix) | |
| 70 -b number: a non-negative number indicating the total number of | |
| 71 pseudo-counts added to each alignment position (default: 1). | |
| 72 Before converting an alignment matrix to a weight matrix, the | |
| 73 total pseudo-counts multiplied by the a priori probability | |
| 74 (see section 3 below) of the corresponding letter is added | |
| 75 to each matrix element. | |
| 76 -v: the matrix is a vertical matrix (default: horizontal matrix). | |
| 77 -p: print the weight matrix derived from the alignment matrix. | |
| 78 | |
| 79 2) -f filename: this file (default: read from the standard input) contains | |
| 80 the names of the sequences. The corresponding sequence may follow | |
| 81 its name if the sequence is enclosed between backslashes (\). | |
| 82 Otherwise, the sequence is assumed to be in a separate file having | |
| 83 the indicated name. | |
| 84 | |
| 85 In the sequences, whitespace, slashes (/), periods, dashes (unless | |
| 86 part of an integer when the "-i" option is used), and comments | |
| 87 beginning with ';', '%', or '#' are ignored. When using letter | |
| 88 characters (i.e., with the "-a" or "-A" alphabet option), integers | |
| 89 are also ignored so that the sequence file can contain positional | |
| 90 information. When using integer characters (i.e., with the "-i" | |
| 91 alphabet option) the integers must be separated by whitespace. | |
| 92 | |
| 93 A "-c" preceding the name of a sequence file indicates that the | |
| 94 corresponding sequence is circular. | |
| 95 | |
| 96 3) Alphabet options---the three options in this section are mutually | |
| 97 exclusive (default: "-a alphabet"). The a priori probabilities mentioned | |
| 98 below are used when converting an alignment matrix to a weight matrix. | |
| 99 -a filename: file containing the alphabet and normalization information. | |
| 100 | |
| 101 Each line contains a letter (a symbol in the alphabet) followed by an | |
| 102 optional normalization number (default: 1.0). The normalization is | |
| 103 based on the relative a priori probabilities of the letters. For | |
| 104 nucleic acids, this might be be the genomic frequency of the bases | |
| 105 or the frequencies observed in the data used to generate the alignment. | |
| 106 In nucleic acid alphabets, a letter and its complement appear on the | |
| 107 same line, separated by a colon (a letter can be its own complement, | |
| 108 e.g. when using a dimer alphabet). Complementary letters may use the | |
| 109 same normalization number. Only the standard 26 letters are | |
| 110 permissible; however, when the "-CS" option is used, the alphabet is | |
| 111 case sensitive so that a total of 52 different characters are possible. | |
| 112 | |
| 113 POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS: | |
| 114 letter | |
| 115 letter normalization | |
| 116 | |
| 117 POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS: | |
| 118 letter:complement | |
| 119 letter:complement normalization | |
| 120 letter:complement normalization:complement's_normalization | |
| 121 | |
| 122 -i filename: same as the "-a" option, except that the symbols of | |
| 123 the alphabet are represented by integers rather than by letters. | |
| 124 Any integer permitted by the machine is a permissible symbol. | |
| 125 | |
| 126 -A alphabet_and_normalization_information: same as "-a" option, except | |
| 127 information appears on the command line (e.g., -A a:t 3 c:g 2). | |
| 128 | |
| 129 4) Alphabet modifiers indicating whether ascii alphabets are case | |
| 130 sensitive---the two options in this section are mutually exclusive | |
| 131 with each other and with the "-i" option (default: ascii alphabets are | |
| 132 case insensitive). | |
| 133 -CS: ascii alphabets are case sensitive. | |
| 134 -CM: ascii alphabets are case insensitive, but mark the location | |
| 135 of lowercase letters by printing a line containing their locations. | |
| 136 This option is useful when lowercase letters indicate a functional | |
| 137 landmark such as a transcriptional start in a DNA sequence. | |
| 138 | |
| 139 5) Options for adjusting or restricting which information | |
| 140 and scores are printed. | |
| 141 The "-ls", "-li", and "-lp" options are mutually exclusive. | |
| 142 -c: also score the complementary sequences. The complements are | |
| 143 determined by the program and are not explicitly stated in the | |
| 144 sequence files. | |
| 145 -ls number: lower threshold for printing scores, inclusive | |
| 146 (formerly the -l option). | |
| 147 -li: assume that the maximum ln(p-value) for printing scores equals | |
| 148 the negative of the sample-size adjusted information content; | |
| 149 indirectly determines the lower threshold for printing scores. | |
| 150 -lp number: the maximum ln(p-value) for printing scores; indirectly | |
| 151 determines the lower threshold for printing scores. | |
| 152 -u number: upper threshold for printing scores, exclusive. | |
| 153 | |
| 154 -t: just print the top score for each sequence. | |
| 155 -t number: print the indicated number of top scores for each sequence. | |
| 156 -ds: if the "-t number" option is used, print the top scores for each | |
| 157 sequence in the order of decreasing score (default: order the | |
| 158 scores according to their position within the sequence). | |
| 159 -e number: the small difference for considering 2 scores equal | |
| 160 (default: 0.000001) | |
| 161 | |
| 162 -s: print the sequence corresponding to each score that is printed. | |
| 163 | |
| 164 6) Options indicating how unrecognized symbols are treated (default: -d1). | |
| 165 Symbols are letters when option "-a" or "-A" is used; | |
| 166 symbols are integers when option "-i" is used. | |
| 167 The following three options are mutually exclusive. | |
| 168 -d0: treat unrecognized symbols as errors and exit the program. | |
| 169 -d1: treat unrecognized symbols as discontinuities, but print a warning. | |
| 170 Treating a symbol as a discontinuity means that any L-mer | |
| 171 containing the unrecognized symbol will be ignored. | |
| 172 -d2: treat unrecognized symbols as discontinuities, and print NO warning. | |
| 173 | |
| 174 7) Options for adjusting the estimation of p-value. | |
| 175 If the -R option is set to zero, the p-value is not estimated. | |
| 176 -R number: the range for approximating a column of the weight matrix with | |
| 177 integers (default: 10000). This number is the difference | |
| 178 between the largest and smallest integers used to estimate | |
| 179 the scores. Higher values increase precision, but will take | |
| 180 longer to calculate the table of p-values. | |
| 181 -M number: the minimum score for approximating p-values (default: 0). | |
| 182 Higher values will increase precision, | |
| 183 but may miss interesting scores. | |
| 184 | |
| 185 | |
| 186 :: | |
| 187 | |
| 188 ---------------------------------------------------------------------- | |
| 189 | |
| 190 Copyright 1990, 1994, 1995, 1996, 2000, 2001, 2002 Gerald Z. Hertz | |
| 191 May be copied for noncommercial purposes. | |
| 192 | |
| 193 Author: | |
| 194 Gerald Z. Hertz | |
| 195 gzhertz AT alum.mit.edu | |
| 196 | |
| 197 PATSER (version 3e) | |
| 198 | |
| 199 This program scores the L-mers (subsequences of length L) of the | |
| 200 indicated sequences against the indicated alignment or weight matrix. | |
| 201 The elements of an alignment matrix are simply the number of times | |
| 202 that the indicated letter is observed at the indicated position of a | |
| 203 sequence alignment. Such elements must be processed before the matrix | |
| 204 can be used to score an L-mer (e.g., Hertz and Stormo, 1999, | |
| 205 Bioinformatics, 15:563-577). A weight matrix is a matrix whose | |
| 206 elements are in a form considered appropriate for scoring an L-mer. | |
| 207 | |
| 208 Each element of an alignment matrix is converted to an element of a | |
| 209 weight matrix by first adding pseudo-counts in proportion to the a | |
| 210 priori probability of the corresponding letter (see option "-b" in | |
| 211 section 1 below) and dividing by the total number of sequences plus | |
| 212 the total number of pseudo-counts. The resulting frequency is | |
| 213 normalized by the a priori probability for the corresponding letter. | |
| 214 The final quotient is converted to an element of a weight matrix by | |
| 215 taking its natural logarithm. The use of pseudo-counts here differs | |
| 216 from previous versions of this program by being proportional to the a | |
| 217 priori probability. | |
| 218 | |
| 219 Version 3 of this program differs from previous versions by also | |
| 220 numerically estimating the p-value of the scores. The p-value | |
| 221 calculated here is the probability of observing a particular score or | |
| 222 higher at a particular sequence position and does NOT account for the | |
| 223 total amount of sequence being scored. P-values are estimated by the | |
| 224 method described in Staden, 1989, CABIOS, p. 89--96. The relative | |
| 225 value for each element of the weight matrix is approximated by | |
| 226 integers in a range determined by the "-R" and "-M" options (section 6 | |
| 227 below). The p-value is calculated for each possible integer score and | |
| 228 the values are stored. The actual scores for the sequences are | |
| 229 determined from the true weight matrix. The true scores are converted | |
| 230 to their corresponding integer values and their p-values are looked up. | |
| 231 | |
| 232 Matrices can be either horizontal or vertical. In a horizontal | |
| 233 matrix, the columns correspond to the positions within the pattern, | |
| 234 and the rows correspond to the letters. Each row begins with the | |
| 235 corresponding letter (or integer, if the "-i" option is used). In a | |
| 236 vertical matrix, the rows correspond to the positions within the | |
| 237 pattern, and the columns correspond to the letters. The first row | |
| 238 contains the letters (or integers, if the "-i" option is used) | |
| 239 corresponding to each column. In both types of matrices, spaces, | |
| 240 tabs, and vertical bars (|) are ignored. The output of the "consensus" | |
| 241 and "wconsensus" programs consists of horizontal alignment matrices. | |
| 242 | |
| 243 The input files can contain comments according to the following | |
| 244 convention. The portion of a line following a ';', '%', or '#' is | |
| 245 considered a comment and is ignored. Comments can begin anywhere in a | |
| 246 line and always end at the end of the line. The output of this | |
| 247 program is sent to the standard output. | |
| 248 | |
| 249 | |
| 250 ]]></help> | |
| 251 <citations> | |
| 252 <citation type="doi">10.1093/bioinformatics/15.7.563</citation> | |
| 253 </citations> | |
| 254 </tool> |