Hi Jen,

First of all, please accept my sincere apology that I forgot to change the email title and made a mess

Maybe I have not explained my question cleared which caused the

confusion: I did not mean the name of dataset. Actually I asked about the display of the tool in the graphic view from the default value (guess it is the name attribute in the tool element of the wrapper) to something else in the workflow editor. As my ultimate purpose is to share my workflow with someone else. If they see three steps with the same displayed name and do not have the related knowledge, they will get lost.

To help myself to explain well, please see the attached illustration.

Best regards!

Jun

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Today's Topics:

1. Question about Extract intron sequences from [gtf file] +

[genome FASTA file] (??)

2. Re: Question about Extract intron sequences from [gtf file] +

[genome FASTA file] (Jennifer Jackson)

3. Re: customize tool display in the workflow (Jun Fan)

4. Re: customize tool display in the workflow (Jennifer Jackson)

5. Very very slow response when a class is using Galaxy from a

computer room in the university (Ido Carmel)

----------------------------------------------------------------------

Message: 1

Date: Wed, 21 Aug 2013 00:29:56 +0800

From: ?? zhusy88@msn.cn

To: galaxy-user@lists.bx.psu.edu

Subject: [galaxy-user] Question about Extract intron sequences from

[gtf file] + [genome FASTA file]

Message-ID: BLU176-DS19B84F8B1D1040DB7AA3E5C4430@phx.gbl

Content-Type: text/plain; charset="gb2312"

Dear Jen,

I am not much of a Galaxy user yet. Some days ago I know something about Galaxy and found it a really wonderful tool. And I am confused by a simple question regarding how to extract intron sequences from [gtf file];

Here is a simple of a gtf file:

1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1";

1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1";

1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1";

1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1";

1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1";

I want to extract intron from the [gtf] file. I found 2 ways may solve the question but it is both useless;

1. I use (Filter and Sort) -> Filter to cut the [gtf] file into 2 files such as the follows:

File A ( contain transcript ):

1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1";

1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1";

File B ( contain exon):

1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1";

1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1";

1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1";

Then I use (Operate on Genomic Intervals)->Subtract to subtract File B from File A Return Non-overlapping pieces of intervals. I thought it will return a file containing intron But the result is an empty file;

2. I convert [gtf] file to [Bed] file ,and use (Extract Features)->Gene BED To Exon/Intron/Codon BED, and it return the same result, an empty file.

I think it must be something wrong with my thoughts. So I really need your help. Thank you very much.

sincerely yours,

John