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#@UGENE_WORKFLOW
#Uses input transcripts and genomic sequences to generate a FASTA file with the DNA sequences for the transcripts.
#Please make sure that contig or chromosome names in the transcript file(s) have corresponding entries in the input sequence(s).
workflow "Extract transcript sequences"{
get-file-list {
type:get-file-list;
name:"Read Sequence(s)";
url-in {
dataset:"Dataset 1";
}
}
get-file-list-1 {
type:get-file-list;
name:"Read Transcripts";
url-in {
dataset:"Dataset 1";
}
}
multiplexer-1 {
type:multiplexer;
name:Multiplexer;
}
gffread {
type:gffread;
name:"Extract Transcript Sequences with Gffread";
url-out:extracted.fa;
}
files-conversion {
type:files-conversion;
name:"To FASTA";
document-format:fasta;
}
files-conversion-1 {
type:files-conversion;
name:"To GTF";
document-format:gtf;
}
.actor-bindings {
get-file-list.out-url->files-conversion.in-file
get-file-list-1.out-url->files-conversion-1.in-file
multiplexer-1.output-data->gffread.in-data
files-conversion.out-file->multiplexer-1.input-data-1
files-conversion-1.out-file->multiplexer-1.input-data-2
}
files-conversion.url->gffread.in-data.genome
files-conversion-1.url->gffread.in-data.transcripts
get-file-list.url->files-conversion.in-file.url
get-file-list-1.url->files-conversion-1.in-file.url
.meta {
visual {
files-conversion {
pos:"-734 -673";
style:simple;
bg-color-simple:"84 84 84 255";
in-file.angle:180;
out-file.angle:360;
}
files-conversion-1 {
pos:"-737 -506";
style:simple;
bg-color-simple:"84 84 84 255";
in-file.angle:180;
out-file.angle:360;
}
get-file-list {
pos:"-940 -672";
style:ext;
bg-color-ext:"24 102 175 64";
bounds:"-30 -30 87 73";
out-url.angle:360;
}
get-file-list-1 {
pos:"-940 -507";
style:ext;
bg-color-ext:"24 102 175 64";
bounds:"-30 -30 86 63";
out-url.angle:360;
}
gffread {
pos:"-420 -644";
style:ext;
bg-color-ext:"208 69 0 64";
bounds:"-30 -30 153 99";
extracted-data.angle:342.973;
in-data.angle:237.6;
}
multiplexer-1 {
pos:"-614 -597";
style:simple;
bg-color-simple:"84 84 84 255";
input-data-1.angle:150;
input-data-2.angle:210;
output-data.angle:360;
}
files-conversion-1.out-file->multiplexer-1.input-data-2 {
text-pos:"-15.3828 -12";
}
files-conversion.out-file->multiplexer-1.input-data-1 {
text-pos:"-16.3828 -28";
}
get-file-list-1.out-url->files-conversion-1.in-file {
text-pos:"-42.3047 -28";
}
get-file-list.out-url->files-conversion.in-file {
text-pos:"-35.3047 -23";
}
multiplexer-1.output-data->gffread.in-data {
text-pos:"-49 -34";
}
}
}
}
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