1#@UGENE_WORKFLOW
2#Create alignment with T-Coffee. T-Coffee is a collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, Protein Sequences. Must have an installed T-Coffee package.
3
4
5
6workflow align-tcoffee{
7
8    tcoffee {
9        type:tcoffee;
10        name:"Align with T-Coffee";
11    }
12    read-msa {
13        type:read-msa;
14        name:"Read alignment";
15        url-in {
16            dataset:"Dataset 1";
17        }
18    }
19    write-msa {
20        type:write-msa;
21        name:"Write alignment";
22    }
23
24
25    .actor-bindings {
26        tcoffee.out-msa->write-msa.in-msa
27        read-msa.out-msa->tcoffee.in-msa
28    }
29
30    read-msa.msa->tcoffee.in-msa.msa
31    tcoffee.msa->write-msa.in-msa.msa
32
33    .meta {
34        parameter-aliases {
35            tcoffee.gap-ext-penalty {
36                alias:gap-ext-penalty;
37                description:"Gap Extension Penalty. Positive values give rewards to gaps and prevent the alignment of unrelated segments (using '0' by default)";
38            }
39            tcoffee.gap-open-penalty {
40                alias:gap-open-penalty;
41                description:"Gap Open Penalty. Must be negative, best matches get a score of 1000 (using '-50' by default)";
42            }
43            tcoffee.iterations-max-num {
44                alias:iter-max;
45                description:"Number of iteration on the progressive alignment: 0 - no iteration (default), -1 - Nseq iterations (using '0' by default)";
46            }
47            tcoffee.path {
48                alias:toolpath;
49                description:"T-Coffee location (using the path specified in UGENE by default)";
50            }
51            tcoffee.temp-dir {
52                alias:tmpdir;
53                description:"Directory to store temporary files (using UGENE temporary directory by default)";
54            }
55            read-msa.url-in {
56                alias:in;
57                description:"Input alignment";
58            }
59            write-msa.document-format {
60                alias:format;
61                description:"Document format of output alignment (using 'clustal' by default)";
62            }
63            write-msa.url-out {
64                alias:out;
65                description:"Output alignment";
66            }
67        }
68        visual {
69            read-msa {
70                pos:"-795 -600";
71                style:ext;
72                bg-color-ext:"0 128 128 64";
73                bounds:"-30 -30 75 102";
74                out-msa.angle:360;
75            }
76            tcoffee {
77                pos:"-585 -600";
78                style:ext;
79                bg-color-ext:"0 128 128 64";
80                bounds:"-30 -30 150 104";
81                in-msa.angle:180;
82                out-msa.angle:360;
83            }
84            write-msa {
85                pos:"-300 -600";
86                style:ext;
87                bg-color-ext:"0 128 128 64";
88                in-msa.angle:180;
89            }
90            read-msa.out-msa->tcoffee.in-msa {
91                text-pos:"-45 -56";
92            }
93            tcoffee.out-msa->write-msa.in-msa {
94                text-pos:"-45 -56";
95            }
96        }
97    }
98}
99
100