1#@UGENE_WORKFLOW
2#Build position weight matrix from existing multiple sequence alignment
3
4
5
6workflow "Build weight matrix"{
7
8    read-msa {
9        type:read-msa;
10        name:"Read alignment";
11        url-in {
12            dataset:"Dataset 1";
13        }
14    }
15    wmatrix-build {
16        type:wmatrix-build;
17        name:"Build weight matrix";
18    }
19    wmatrix-write {
20        type:wmatrix-write;
21        name:"Write weight matrix";
22    }
23
24
25    .actor-bindings {
26        read-msa.out-msa->wmatrix-build.in-msa
27        wmatrix-build.out-wmatrix->wmatrix-write.in-wmatrix
28    }
29
30    read-msa.msa->wmatrix-build.in-msa.msa
31    wmatrix-build.wmatrix->wmatrix-write.in-wmatrix.wmatrix
32
33    .meta {
34        parameter-aliases {
35            read-msa.url-in {
36                alias:in;
37                description:"Input alignment";
38            }
39            wmatrix-build.matrix-type {
40                alias:type;
41                description:"Weight matrix type (using 'Mononucleic' by default)";
42            }
43            wmatrix-build.weight-algorithm {
44                alias:algo;
45                description:"Weight algorithm (using 'Berg and von Hippel' by default)";
46            }
47            wmatrix-write.url-out {
48                alias:out;
49                description:"Output weight matrix";
50            }
51        }
52        visual {
53            read-msa {
54                pos:"-780 -690";
55                style:ext;
56                bg-color-ext:"0 128 128 64";
57                out-msa.angle:360;
58            }
59            wmatrix-build {
60                pos:"-570 -690";
61                style:ext;
62                bg-color-ext:"0 128 128 64";
63                in-msa.angle:180;
64                out-wmatrix.angle:360;
65            }
66            wmatrix-write {
67                pos:"-375 -690";
68                style:ext;
69                bg-color-ext:"0 128 128 64";
70                in-wmatrix.angle:180;
71            }
72            read-msa.out-msa->wmatrix-build.in-msa {
73                text-pos:"-45 -50";
74            }
75            wmatrix-build.out-wmatrix->wmatrix-write.in-wmatrix {
76                text-pos:"-37.5 -24";
77            }
78        }
79    }
80}
81
82