1#@UGENE_WORKFLOW
2#Build hmm profile using hmmer2
3
4
5
6workflow hmm2-build{
7
8    read-msa {
9        type:read-msa;
10        name:"Read alignment";
11        url-in {
12            dataset:"Dataset 1";
13        }
14    }
15    hmm2-build {
16        type:hmm2-build;
17        name:"HMM build";
18    }
19    hmm2-write-profile {
20        type:hmm2-write-profile;
21        name:"Write HMM profile";
22    }
23
24
25    .actor-bindings {
26        read-msa.out-msa->hmm2-build.in-msa
27        hmm2-build.out-hmm2->hmm2-write-profile.in-hmm2
28    }
29
30    read-msa.msa->hmm2-build.in-msa.msa
31    hmm2-build.hmm2-profile->hmm2-write-profile.in-hmm2.hmm2-profile
32
33    .meta {
34        parameter-aliases {
35            read-msa.url-in {
36                alias:in;
37                description:"Input alignment";
38            }
39            hmm2-build.calibrate {
40                alias:calibrate;
41                description:"Enables/disables optional profile calibration (using 'True' by default)";
42            }
43            hmm2-build.calibration-threads {
44                alias:parallel-calibration;
45                description:"Number of parallel threads that the calibration will run in (using '1' by default)";
46            }
47            hmm2-build.deviation {
48                alias:stand-deviation;
49                description:"Standard deviation of the synthetic sequence length. A positive number. The default is 200. Note that the Gaussian is left-truncated so that no sequences have lengths (using '200.00' by default)";
50            }
51            hmm2-build.fix-samples-length {
52                alias:fixed-length;
53                description:"Fix the length of the random sequences to , where is a positive (and reasonably sized) integer. The default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution (using '0' by default)";
54            }
55            hmm2-build.mean-samples-length {
56                alias:mean-length;
57                description:"Mean length of the synthetic sequences, positive real number. The default value is 325 (using '325' by default)";
58            }
59            hmm2-build.profile-name {
60                alias:name;
61                description:"Name of the profile HMM (using 'hmm_profile' by default)";
62            }
63            hmm2-build.samples-num {
64                alias:samples-count;
65                description:"Number of synthetic sequences. If is less than about 1000, the fit to the EVD may fail Higher numbers of will give better determined EVD parameters. The default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time (using '0' by default)";
66            }
67            hmm2-build.seed {
68                alias:seed;
69                description:"The seed for random numbers (using '0' by default)";
70            }
71            hmm2-build.strategy {
72                alias:strategy;
73                description:"Specifies kind of alignments you want to allow (using 'hmmls' by default)";
74            }
75            hmm2-write-profile.url-out {
76                alias:out;
77                description:"Output profile HMM";
78            }
79        }
80        visual {
81            hmm2-build {
82                pos:"-555 -660";
83                style:ext;
84                bg-color-ext:"0 128 128 64";
85                in-msa.angle:180;
86                out-hmm2.angle:360;
87            }
88            hmm2-write-profile {
89                pos:"-360 -660";
90                style:ext;
91                bg-color-ext:"0 128 128 64";
92                in-hmm2.angle:180;
93            }
94            read-msa {
95                pos:"-750 -660";
96                style:ext;
97                bg-color-ext:"0 128 128 64";
98                out-msa.angle:360;
99            }
100            hmm2-build.out-hmm2->hmm2-write-profile.in-hmm2 {
101                text-pos:"-32 -24";
102            }
103            read-msa.out-msa->hmm2-build.in-msa {
104                text-pos:"-45 -50";
105            }
106        }
107    }
108}
109
110