1#@UGENE_WORKFLOW
2#Create alignment with ClustalO. ClustalO is a general purpose multiple sequence alignment program for proteins. Must have an installed ClustalO package.
3
4
5
6workflow align-clustalo{
7
8    read-msa {
9        type:read-msa;
10        name:"Read alignment";
11        url-in {
12            dataset:"Dataset 1";
13        }
14    }
15    write-msa {
16        type:write-msa;
17        name:"Write alignment";
18    }
19    ClustalO {
20        type:ClustalO;
21        name:"Align with ClustalO";
22    }
23
24
25    .actor-bindings {
26        read-msa.out-msa->ClustalO.in-msa
27        ClustalO.out-msa->write-msa.in-msa
28    }
29
30    ClustalO.msa->write-msa.in-msa.msa
31    read-msa.msa->ClustalO.in-msa.msa
32
33    .meta {
34        parameter-aliases {
35            read-msa.url-in {
36                alias:in;
37                description:"Input alignment";
38            }
39            write-msa.document-format {
40                alias:format;
41                description:"Document format of output alignment (using 'clustal' by default)";
42            }
43            write-msa.url-out {
44                alias:out;
45                description:"Output alignment";
46            }
47            ClustalO.max-guidetree-iterations {
48                alias:max-guidetree-iterations;
49                description:"Maximum number guidetree iterations (using '0' by default)";
50            }
51            ClustalO.max-hmm-iterations {
52                alias:max-hmm-iterations;
53                description:"Maximum number of HMM iterations (using '0' by default)";
54            }
55            ClustalO.num-iterations {
56                alias:iter;
57                description:"Number of (combined guide-tree/HMM) iterations (using '1' by default)";
58            }
59            ClustalO.path {
60                alias:toolpath;
61                description:"ClustalO location (using the path specified in UGENE by default)";
62            }
63            ClustalO.set-auto {
64                alias:auto;
65                description:"Set options automatically (might overwrite some of your options) (using 'False' by default)";
66            }
67            ClustalO.temp-dir {
68                alias:tmpdir;
69                description:"Directory to store temporary files (using UGENE temporary directory by default)";
70            }
71        }
72        visual {
73            ClustalO {
74                pos:"-540 -645";
75                style:ext;
76                bg-color-ext:"0 128 128 64";
77                in-msa.angle:180;
78                out-msa.angle:360;
79            }
80            read-msa {
81                pos:"-735 -645";
82                style:ext;
83                bg-color-ext:"0 128 128 64";
84                out-msa.angle:360;
85            }
86            write-msa {
87                pos:"-330 -645";
88                style:ext;
89                bg-color-ext:"0 128 128 64";
90                in-msa.angle:180;
91            }
92            ClustalO.out-msa->write-msa.in-msa {
93                text-pos:"-45 -39";
94            }
95            read-msa.out-msa->ClustalO.in-msa {
96                text-pos:"-58 -39";
97            }
98        }
99    }
100}
101
102