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#@UGENE_WORKFLOW
#This schema allows one to analyze sequence with Query and save results as alignment of selected features.
#To execute the workflow do the following:
#1) Select "Sequence Reader" task and specify source file at "URL" field in the Property Editor.
#2) Select "Annotate with UQL" task and specify the URL of the UQL schema file.
#3) Select "Filter annotations by name" task and specify the name of features to be joined into alignment.
#4) Select "Join sequences into alignment" task and specify the URL of the result file.
#
workflow "Convert UQL schema results to alignment" {
read-sequence {
type:read-sequence;
name:"Read sequence";
merge-gap:10;
mode:0;
}
query {
type:query;
name:"Annotate with UQL";
merge:false;
offset:0;
}
extract-annotated-sequence {
type:extract-annotated-sequence;
name:"Get sequences by annotations";
complement:true;
extend-left:0;
extend-right:0;
merge-gap-length:1;
translate:false;
}
sequences-to-msa {
type:sequences-to-msa;
name:"Join sequences into alignment";
}
write-msa {
type:write-msa;
name:"Write alignment";
document-format:clustal;
write-mode:2;
url-out:output.aln;
}
filter-annotations {
type:filter-annotations;
name:"Filter annotations by name";
accept-or-filter:true;
}
read-sequence.sequence->query.in-sequence.sequence
filter-annotations.annotations->extract-annotated-sequence.in-sequence.annotations
read-sequence.sequence->extract-annotated-sequence.in-sequence.sequence
extract-annotated-sequence.sequence->sequences-to-msa.in-sequence.sequence
sequences-to-msa.msa->write-msa.in-msa.msa
query.annotations->filter-annotations.in-annotations.annotations
.meta {
visual {
read-sequence {
pos:"-765 -795";
style:ext;
bg-color-ext:"0 128 128 64";
out-sequence.angle:360;
}
query {
pos:"-615 -795";
style:ext;
bg-color-ext:"0 128 128 64";
bounds:"-30 -30 75 91";
in-sequence.angle:180;
out-annotations.angle:360;
}
read-sequence.out-sequence->query.in-sequence {
text-pos:"-27.5 -24";
}
extract-annotated-sequence {
pos:"-255 -795";
style:ext;
bg-color-ext:"0 128 128 64";
bounds:"-30 -30 116 105";
in-sequence.angle:183.18;
out-sequence.angle:294.642;
}
sequences-to-msa {
pos:"-255 -585";
style:ext;
bg-color-ext:"0 128 128 64";
in-sequence.angle:45;
out-msa.angle:291.49;
}
extract-annotated-sequence.out-sequence->sequences-to-msa.in-sequence {
text-pos:"-45 -37";
}
write-msa {
pos:"-240 -390";
style:ext;
bg-color-ext:"0 128 128 64";
in-msa.angle:73.0725;
}
sequences-to-msa.out-msa->write-msa.in-msa {
text-pos:"-43.5 -24";
}
filter-annotations {
pos:"-475 -795";
style:ext;
bg-color-ext:"0 128 128 64";
in-annotations.angle:180;
out-annotations.angle:360;
}
query.out-annotations->filter-annotations.in-annotations {
text-pos:"-45 -37";
}
filter-annotations.out-annotations->extract-annotated-sequence.in-sequence {
text-pos:"-45 -37";
}
}
wizard {
name:"Convert UQL schema results to alignment Wizard";
help-page-id:16122706;
auto-run: true;
page {
id:1;
next:2;
title:"Input sequence(s)";
parameters-area {
read-sequence.url-in {
type:datasets;
}
}
}
page {
id:2;
title:"Annotate with UQL";
parameters-area {
group {
title:"UQL parameters";
label-size:120;
query.url-in {
label:"UQL schema file";
}
query.merge {
}
query.offset {
}
}
group {
title:"Filter annotations parameters";
label-size:120;
filter-annotations.annotation-names {
}
filter-annotations.accept-or-filter {
}
}
group {
title:"Output data";
label-size:120;
write-msa.url-out {
label:"Result file";
}
write-msa.document-format {
}
}
}
}
}
}
}
|
