1#@UGENE_WORKFLOW
2#Search for transcription factor binding sites (TFBS) with position frequency matrices
3
4
5
6workflow "Search frequency matrix"{
7
8    read-sequence {
9        type:read-sequence;
10        name:"Read sequence";
11        url-in {
12            dataset:"Dataset 1";
13        }
14    }
15    fmatrix-read {
16        type:fmatrix-read;
17        name:"Read frequency matrix";
18    }
19    fmatrix-to-wmatrix {
20        type:fmatrix-to-wmatrix;
21        name:"Convert frequency matrix";
22    }
23    wmatrix-search {
24        type:wmatrix-search;
25        name:"Search for TFBS with weight matrix";
26        strand:0;
27    }
28    write-genbank {
29        type:write-sequence;
30        name:"Write Genbank";
31        document-format:genbank;
32    }
33
34
35    .actor-bindings {
36        read-sequence.out-sequence->wmatrix-search.in-sequence
37        fmatrix-read.out-fmatrix->fmatrix-to-wmatrix.in-fmatrix
38        fmatrix-to-wmatrix.out-wmatrix->wmatrix-search.in-wmatrix
39        wmatrix-search.out-annotations->write-genbank.in-sequence
40    }
41
42    fmatrix-read.fmatrix->fmatrix-to-wmatrix.in-fmatrix.fmatrix
43    read-sequence.sequence->wmatrix-search.in-sequence.sequence
44    fmatrix-to-wmatrix.wmatrix->wmatrix-search.in-wmatrix.wmatrix
45    wmatrix-search.annotations->write-genbank.in-sequence.annotations
46    read-sequence.annotations->write-genbank.in-sequence.annotations
47    read-sequence.sequence->write-genbank.in-sequence.sequence
48
49    .meta {
50        parameter-aliases {
51            read-sequence.url-in {
52                alias:seq;
53                description:"Input sequence";
54            }
55            fmatrix-read.url-in {
56                alias:matrix;
57                description:"Input frequency matrix";
58            }
59            fmatrix-to-wmatrix.matrix-type {
60                alias:type;
61                description:"Matrix type (using 'Mononucleic' by default)";
62            }
63            fmatrix-to-wmatrix.weight-algorithm {
64                alias:algo;
65                description:"Weight algorithm (using 'Berg and von Hippel' by default)";
66            }
67            wmatrix-search.min-score {
68                alias:score;
69                description:"Minimum score to detect transcription factor binding site (using '85' percents by default)";
70            }
71            wmatrix-search.result-name {
72                alias:annotation-name;
73                description:"Annotation name for marking found regions (using 'misc_feature' by default)";
74            }
75            wmatrix-search.strand {
76                alias:strand;
77                description:"Search strand";
78            }
79            write-genbank.accumulate {
80                alias:accumulate;
81                description:"Accumulate all incoming data in one file or create separate files for each input. In the latter case, an incremental numerical suffix is added to the file name (using 'True' by default)";
82            }
83            write-genbank.url-out {
84                alias:out;
85                description:"Output file with annotations";
86            }
87        }
88        visual {
89            fmatrix-read {
90                pos:"-750 -435";
91                style:ext;
92                bg-color-ext:"0 128 128 64";
93                out-fmatrix.angle:360;
94            }
95            fmatrix-to-wmatrix {
96                pos:"-540 -435";
97                style:ext;
98                bg-color-ext:"0 128 128 64";
99                in-fmatrix.angle:180;
100                out-wmatrix.angle:76.6075;
101            }
102            read-sequence {
103                pos:"-780 -645";
104                style:ext;
105                bg-color-ext:"0 128 128 64";
106                out-sequence.angle:360;
107            }
108            wmatrix-search {
109                pos:"-585 -645";
110                style:ext;
111                bg-color-ext:"0 128 128 64";
112                in-sequence.angle:150;
113                in-wmatrix.angle:291.389;
114                out-annotations.angle:360;
115            }
116            write-genbank {
117                pos:"-285 -645";
118                style:ext;
119                bg-color-ext:"0 128 128 64";
120                in-sequence.angle:180;
121            }
122            fmatrix-read.out-fmatrix->fmatrix-to-wmatrix.in-fmatrix {
123                text-pos:"-45 -37";
124            }
125            fmatrix-to-wmatrix.out-wmatrix->wmatrix-search.in-wmatrix {
126                text-pos:"-37.5 -24";
127            }
128            read-sequence.out-sequence->wmatrix-search.in-sequence {
129                text-pos:"-27.5 -24";
130            }
131            wmatrix-search.out-annotations->write-genbank.in-sequence {
132                text-pos:"-45 -37";
133            }
134        }
135    }
136}
137
138