#@UGENE_WORKFLOW
workflow "Filter by motif"{
read-sequence {
type:read-sequence;
name:"Read Sequence";
}
search {
type:search;
name:"Find Substrings";
result-name:motif_of_interest;
}
mark-sequence {
type:mark-sequence;
name:"Sequence Marker";
markers:m1;
}
filter-by-values {
type:filter-by-values;
name:Filter;
text:HasMotifs;
}
write-sequence {
type:write-sequence;
name:"Write Sequence";
document-format:genbank;
}
@mark-sequence.m1 {
type:marker;
marker-type:annotations-count;
marker-name:CountMotifs;
annotation-name:motif_of_interest;
">=1":HasMotifs;
"rest":Rest;
}
.actor-bindings {
search.out-annotations->mark-sequence.in-sequence
mark-sequence.out-marked-seq->filter-by-values.in-data
filter-by-values.filtered-data->write-sequence.in-sequence
read-sequence.out-sequence->search.in-sequence
}
read-sequence.sequence->search.in-sequence.sequence
read-sequence.annotations->mark-sequence.in-sequence.annotations
search.annotations->mark-sequence.in-sequence.annotations
read-sequence.sequence->mark-sequence.in-sequence.sequence
mark-sequence.CountMotifs->filter-by-values.in-data.text
read-sequence.annotations->write-sequence.in-sequence.annotations {
path-through:filter-by-values;
}
read-sequence.sequence->write-sequence.in-sequence.sequence {
path-through:filter-by-values;
}
.meta {
visual {
read-sequence {
description:" Read Sequence
Reads sequence(s) from unset.
";
tooltip:"Reads sequences and annotations if any from local or remote files.";
pos:"-885 -630";
style:ext;
bg-color-ext:"0 128 128 64";
out-sequence.angle:360;
}
search {
description:" Find Substrings
Searches regions in each sequence from Read Sequence similar to unset pattern(s).
A substring must match a pattern exactly.
Searches in both strands of a sequence. Outputs the regions found annotated as motif_of_interest.
";
tooltip:"Searches regions in a sequence similar to a pattern sequence. Outputs a set of annotations.";
pos:"-675 -630";
style:ext;
bg-color-ext:"0 128 128 64";
in-sequence.angle:180;
out-annotations.angle:360;
}
read-sequence.out-sequence->search.in-sequence {
text-pos:"-27.5 -24";
}
mark-sequence {
description:" Sequence Marker
Adds one or several marks to the input sequence.
";
tooltip:"Adds one or several marks to the input sequence depending on the sequence properties. Use this element, for example, in conjunction with the Filter element.";
pos:"-345 -630";
style:ext;
bg-color-ext:"0 128 128 64";
in-sequence.angle:180;
out-marked-seq.angle:51.953;
}
search.out-annotations->mark-sequence.in-sequence {
text-pos:"-45 -37";
}
filter-by-values {
description:" Filter
Filters input data from Sequence Marker by value(s) HasMotifs.
";
tooltip:"Passes through only data that matches the input filter value (or values).";
pos:"-345 -840";
style:ext;
bg-color-ext:"0 128 128 64";
in-data.angle:285.306;
filtered-data.angle:360;
}
mark-sequence.out-marked-seq->filter-by-values.in-data {
text-pos:"-47 -23";
}
write-sequence {
description:" Write Sequence
Save all sequences from Read Sequence to unset.
";
tooltip:"Writes all supplied sequences to file(s) in selected format.";
pos:"-135 -840";
style:ext;
bg-color-ext:"0 128 128 64";
in-sequence.angle:180;
}
filter-by-values.filtered-data->write-sequence.in-sequence {
text-pos:"-34 -24";
}
}
}
}