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#@UGENE_WORKFLOW
#Performs multiple sequence alignment with MUSCLE algorithm and saves the resulting alignment to document. Source data can be of any format containing sequences or alignments.
#
#To use this workflow, you need to specify locations for input and output file(s). To do this, select a corresponding task, so its' parameters appear in Property Inspector panel, and specify desired value(s) for "URL" parameter. Then you can launch the workflow with pressing Ctrl+R keys.
workflow "Align sequences with MUSCLE"{
read-msa {
type:read-msa;
name:"Read alignment";
}
muscle {
type:muscle;
name:"Align with MUSCLE";
}
write-msa {
type:write-msa;
name:"Write alignment";
document-format:clustal;
url-out:muscle_alignment.aln;
}
.actor-bindings {
read-msa.out-msa->muscle.in-msa
muscle.out-msa->write-msa.in-msa
}
read-msa.msa->muscle.in-msa.msa
muscle.msa->write-msa.in-msa.msa
.meta {
visual {
read-msa {
pos:"-645 -555";
style:ext;
bg-color-ext:"0 128 128 64";
out-msa.angle:360;
}
muscle {
pos:"-480 -555";
style:ext;
bg-color-ext:"0 128 128 64";
in-msa.angle:180;
out-msa.angle:360;
}
write-msa {
pos:"-240 -555";
style:ext;
bg-color-ext:"0 128 128 64";
in-msa.angle:180;
}
read-msa.out-msa->muscle.in-msa {
text-pos:"-45 -50";
}
muscle.out-msa->write-msa.in-msa {
text-pos:"-45 -50";
}
}
wizard {
name:"Align Sequences with MUSCLE Wizard";
help-page-id:16122700;
auto-run: true;
page {
id:1;
next:2;
title:"Input MSA(s)";
parameters-area {
read-msa.url-in {
type:datasets;
}
}
}
page {
id:2;
title:"Align Sequences with MUSCLE";
parameters-area {
group {
title:"MUSCLE Algorithm parameters";
label-size:120;
muscle.mode {
}
muscle.stable {
}
muscle.max-iterations {
}
muscle.range {
}
}
group {
title:"Output File";
label-size:120;
write-msa.url-out {
label:"Result alignment";
}
write-msa.document-format {
}
}
}
}
}
}
}
|
