1#@UGENE_WORKFLOW
2#Run local NCBI BLAST search. BLAST finds regions of similarity between biological sequences. Must have an installed NCBI BLAST package.
3
4
5
6workflow local-blast+{
7
8    read-sequence {
9        type:read-sequence;
10        name:"Read sequence";
11        url-in {
12            dataset:"Dataset 1";
13        }
14    }
15    write-genbank {
16        type:write-sequence;
17        name:"Write Genbank";
18        document-format:genbank;
19    }
20    blast-plus {
21        type:blast-plus;
22        name:"Local BLAST+ search";
23    }
24
25
26    .actor-bindings {
27        read-sequence.out-sequence->blast-plus.in-sequence
28        blast-plus.out-annotations->write-genbank.in-sequence
29    }
30
31    blast-plus.annotations->write-genbank.in-sequence.annotations
32    read-sequence.annotations->write-genbank.in-sequence.annotations
33    read-sequence.sequence->write-genbank.in-sequence.sequence
34    read-sequence.sequence->blast-plus.in-sequence.sequence
35
36    .meta {
37        parameter-aliases {
38            read-sequence.url-in {
39                alias:in;
40                description:"Input sequence";
41            }
42            write-genbank.accumulate {
43                alias:accumulate;
44                description:"Accumulate all incoming data in one file or create separate files for each input. In the latter case, an incremental numerical suffix is added to the file name (using 'True' by default)";
45            }
46            write-genbank.url-out {
47                alias:out;
48                description:"Output file with annotations";
49            }
50            blast-plus.blast-output {
51                alias:blast-out;
52                description:"Location of BLAST output file";
53            }
54            blast-plus.blast-type {
55                alias:p;
56                description:"Type of BLAST searches (using 'blastn' by default)";
57            }
58            blast-plus.db-name {
59                alias:dbname;
60                description:"Base name for BLAST DB files";
61            }
62            blast-plus.db-path {
63                alias:dbpath;
64                description:"Path with database files";
65            }
66            blast-plus.e-val {
67                alias:e;
68                description:"The statistical significance threshold for reporting matches against database sequences (using '10.0' by default)";
69            }
70            blast-plus.max-hits {
71                alias:max-hits;
72                description:"If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit.";
73            }
74            blast-plus.gapped-aln {
75                alias:gap-aln;
76                description:"Perform gapped alignment (using 'use' by default)";
77            }
78            blast-plus.result-name {
79                alias:name;
80                description:"Name of the result annotations marking found regions (using 'blast_result' by default)";
81            }
82            blast-plus.temp-dir {
83                alias:tmpdir;
84                description:"Directory to store temporary files (using UGENE temporary directory by default)";
85            }
86            blast-plus.tool-path {
87                alias:toolpath;
88                description:"BLAST+ location (using the path specified in UGENE by default)";
89            }
90            blast-plus.type-output {
91                alias:blast-out-type;
92                description:"Type of BLAST output file (using 'XML (-outfmt 5)' by default)";
93            }
94            blast-plus.comp-based-stats {
95                alias:comp-based-stats;
96                description:"Composition-based statistics: D (default, equal to 2), 0, 1, 2 or 3.";
97            }
98        }
99        visual {
100            blast-plus {
101                pos:"-585 -615";
102                style:ext;
103                bg-color-ext:"0 128 128 64";
104                in-sequence.angle:180;
105                out-annotations.angle:360;
106            }
107            read-sequence {
108                pos:"-765 -615";
109                style:ext;
110                bg-color-ext:"0 128 128 64";
111                out-sequence.angle:360;
112            }
113            write-genbank {
114                pos:"-330 -615";
115                style:ext;
116                bg-color-ext:"0 128 128 64";
117                in-sequence.angle:180;
118            }
119            blast-plus.out-annotations->write-genbank.in-sequence {
120                text-pos:"-33 -24";
121            }
122            read-sequence.out-sequence->blast-plus.in-sequence {
123                text-pos:"-27.5 -24";
124            }
125        }
126    }
127}
128
129