Hi, this is what had happened: I'm testing on the integration of ttuner into the UGENE workflow designer:

The workflow are as the first screenshot:
Read abi sequence > ttuner1 > ttuner2 > Write sequence

ttuner1: ttuner -sa $outfile -if $infile
$infile : Sequence (GFF)
$outfile: Sequence (FASTA)

ttuner2: ttuner -qa $outfile -if $infile
$infile : Sequence (GFF)
$outfile : Sequence (FASTA)

This works well when I wrote hard code with the path to the input files, but when I change it to URL input it does not work.

Kindly advice, thanks!

Regards,
Kenneth

I can comment your problems.

1) First of all, I should tell about the second schema. As I can see, your execution string is "ttuner -sa $seq -id $in". The ttuner cmdline key "-id" means that you put a directory to the input. But the "Read sequence" element reads files, and only sequence data will be available in the output port, but not any directories.

2) I have finally understood why your and PEH's attempts for using parameters doesn't work We call different things by one name (parameter). As I understand, you talk about cmdline parameters ($out, $in, ...). But I talk about Workflow element's parameters (see a screenshot). I will show how to use them.

And what about your first schema. I have already told about using ABI files in Workflow.
a) So far Workflow Designer doesn't support working with chromatogram data. When "Read Sequence" element reads an ABI file, containing both sequence and chromatogram, only sequence data will available in the output port.
b) So, when you set up a cmdline element's port you can choose only 4 formats for this port (Fasta, Fastq, GFF, Genbank). And if you want to set up your custom element for getting a sequence data from an input port, you should correctly set the execution string too (for example, be sure that $in is able to be a file with the port specified format).

I know that it is not so simple and clear, but your task is complex too (you want to unite together the work of two independent applications)

3) How can I help you? Please, look at my post
http://ugene.unipro.ru/forum/YaBB.pl?num=1326766085/0#6
You can create a custom element that would have no input ports and have output sequence port $out_seq (with the fasta format). Also, it would have a URL parameter $fof (Workflow element parameter  ). fof would store a url for a file of files. And the execution string would be: "ttuner -if $fof -sa $out_seq".

This element gets a file of files from the parameter, launches ttuner (that creates an output fasta file) and puts sequences to the output port.

Hi German, thanks for your clarification but unfortunately it still does not work. Please see screen shots.

Besides, will future release of UGENE WD support chromatogram data? Kindly advice, thanks!

Kenneth, see the attachment, please. There is an example of the input file, that you need to put to your $www parameter.

Check, that I wrote the correct url

kenkl wrote on Feb 14^th, 2012 at 3:18pm:


Good job!
About chromatograms: currently UGENE has no any functionality for working with chromatograms, you can just open an ABI file and see the content of the file. So, Workflow Designer has no elements for working with chromatograms too.

In next releases UGENE will not support chromatogram datatype in Workflow.

But we have planned this feature for some future releases:
https://ugene.unipro.ru/tracker/browse/UGENE-838

We will be appreciate if you tell us what functionality is needed by biologist for working with chromatograms and that we could implement in UGENE. It is better to write at "Feature Requests" forum:
http://ugene.unipro.ru/forum/YaBB.pl?board=feature

kenkl wrote on Feb 15^th, 2012 at 4:30pm:

You are able to convert ABI to FASTA (or other formats) now, without any additional supporting and tools. Just make a scheme in Workflow Designer:

Read Sequence -> Write Fasta

Put your ABI files to the "Input file(s)" parameter of the "Read sequence" element. And set the output filename for the "Write Fasta" element. And you will receive the data in the needed useful format.

kenkl wrote on Feb 16^th, 2012 at 10:43am:

For keeping quality scores you can choose the FASTQ format.
Read Sequence -> Write Sequence
And choose "fastq" in the format property of the "Write Sequence" element.

What about the second question... Currently, it is not possible. But could you describe me a purpose of it? What different 2 input data and what external tool do you want to use? It is important for me to know about it for clear understanding the problem and finding the best solution.

Kenneth, thanks for your feedback.
It is very good that you tell us about needed features, because they are useful and we should implement them.

Yes, your scheme shows that several slots supporting is needed for some cmdline tools. I have created an issue at our bug tracker:
https://ugene.unipro.ru/tracker/browse/UGENE-843

It will be fixed asap.