1#@UGENE_WORKFLOW
2#Builds statistical profile for SITECON. The SITECON is a program for probabilistic recognition of transcription factor binding sites.
3
4
5
6workflow sitecon-build{
7
8    read-msa {
9        type:read-msa;
10        name:"Read alignment";
11        url-in {
12            dataset:"Dataset 1";
13        }
14    }
15    sitecon-build {
16        type:sitecon-build;
17        name:"Build SITECON model";
18    }
19    sitecon-write {
20        type:sitecon-write;
21        name:"Write SITECON model";
22    }
23
24
25    .actor-bindings {
26        read-msa.out-msa->sitecon-build.in-msa
27        sitecon-build.out-sitecon->sitecon-write.in-sitecon
28    }
29
30    read-msa.msa->sitecon-build.in-msa.msa
31    sitecon-build.sitecon-model->sitecon-write.in-sitecon.sitecon-model
32
33    .meta {
34        parameter-aliases {
35            read-msa.url-in {
36                alias:in;
37                description:"Input alignment";
38            }
39            sitecon-build.calibrate-length {
40                alias:clength;
41                description:"Length of random synthetic sequences used to calibrate the profile (using '1000000' by default)";
42            }
43            sitecon-build.seed {
44                alias:rseed;
45                description:"The seed for random numbers (using '0' by default)";
46            }
47            sitecon-build.weight-algorithm {
48                alias:walg;
49                description:"Weight algorithm (using 'False' by default)";
50            }
51            sitecon-build.window-size {
52                alias:wsize;
53                description:"Window size, bp (using '40' by default)";
54            }
55            sitecon-write.url-out {
56                alias:out;
57                description:"Output SITECON model";
58            }
59        }
60        visual {
61            read-msa {
62                pos:"-765 -675";
63                style:ext;
64                bg-color-ext:"0 128 128 64";
65                out-msa.angle:360;
66            }
67            sitecon-build {
68                pos:"-570 -675";
69                style:ext;
70                bg-color-ext:"0 128 128 64";
71                in-msa.angle:180;
72                out-sitecon.angle:360;
73            }
74            sitecon-write {
75                pos:"-345 -675";
76                style:ext;
77                bg-color-ext:"0 128 128 64";
78                in-sitecon.angle:180;
79            }
80            read-msa.out-msa->sitecon-build.in-msa {
81                text-pos:"-45 -50";
82            }
83            sitecon-build.out-sitecon->sitecon-write.in-sitecon {
84                text-pos:"-37 -24";
85            }
86        }
87    }
88}
89
90