Question: Customize Tool Display In The Workflow
0
gravatar for Jun Fan
4.9 years ago by
Jun Fan50
Jun Fan50 wrote:
Dear Galaxy develop team: Normally I generate the workflow from history. It works fine except one annoying problem: the display of step/tool is just the tool name, which can cause confusion in a big workflow. For example, I have a mixture of samples from multiple species and do the BLAST against Human, Virus, Mouse etc which will call BLAST several times. To make results distinguishable, I will rename the dataset in the history. But this will be lost when creating workflow from history. The workflow will have duplicate steps named as BLAST while I really want to have steps displayed as BLAST against Human etc. Could you tell me whether I have done something wrong? If not, could you kindly add this functionality into the new release of Galaxy? If it is possible to customize the tool display in the workflow, how to write the wrapper as setting the label to allow this? Best regards! Jun
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ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Jun Fan50
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gravatar for Jennifer Hillman Jackson
4.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Jun, I asked Dannon (our workflow lead developer) and he suggested just using the existing workflow datastet renaming functions. These are in the right panel when you click on a dataset within the workflow editor (as you probably know). Inherited naming is not something that is currently being worked on, but you can always start a Trello card and see if it gathers votes or the attention of a contributor from the larger development community: http://wiki.galaxyproject.org/Support#Galaxy_Issue_Board Take care, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENTlink written 4.9 years ago by Jennifer Hillman Jackson25k
0
gravatar for Jun Fan
4.9 years ago by
Jun Fan50
Jun Fan50 wrote:
Hi Jennifer, Many thanks for your reply. Unfortunately I am not clever to figure out how to using the existing workflow dataset renaming functions. I only know how to rename a dataset within history. Could you show me how to do this? I have attached a screen shot of my workflow. You can see that I have only managed to add annotation/notes to this step. Ideally I would like to have the step with the label of "mzidLib:PostProcessing FDR" in the graphic view. From other thread, someone mentioned to use ${method} in the label, I failed to apply this trick. Best regards! Jun Message: 3 Date: Mon, 19 Aug 2013 10:18:32 -0700 To: Jun Fan <j.fan@qmul.ac.uk> Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] customize tool display in the workflow Message-ID: <52125368.1060308@bx.psu.edu> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" Hi Jun, I asked Dannon (our workflow lead developer) and he suggested just using the existing workflow datastet renaming functions. These are in the right panel when you click on a dataset within the workflow editor (as you probably know). Inherited naming is not something that is currently being worked on, but you can always start a Trello card and see if it gathers votes or the attention of a contributor from the larger development community: http://wiki.galaxyproject.org/Support#Galaxy_Issue_Board Take care, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org URL: <http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130819="" 8dca342d="" attachment-0001.html=""> _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ End of galaxy-user Digest, Vol 86, Issue 16 *******************************************
ADD COMMENTlink written 4.9 years ago by Jun Fan50
Hi Jun, You are very close - just click on the "create" button within the "Edit Step Actions" box and it will expand, where you can then enter the new custom name. It will look something like this: The other post you are referring to is a method to name the output dataset based on the input datasets name. You can certainly try this out and see if it is useful. Hope this helps, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD REPLYlink written 4.9 years ago by Jennifer Hillman Jackson25k
0
gravatar for Jun Fan
4.9 years ago by
Jun Fan50
Jun Fan50 wrote:
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 [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of galaxy-user-request@lists.bx.psu.edu To: galaxy-user@lists.bx.psu.edu Subject: galaxy-user Digest, Vol 86, Issue 17 Send galaxy-user mailing list submissions to galaxy-user@lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-user or, via email, send a message with subject or body 'help' to galaxy-user-request@lists.bx.psu.edu You can reach the person managing the list at galaxy-user-owner@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-user digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. 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 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 URL: <http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130821="" 0686d76a="" attachment-0001.html=""> Message: 2 Date: Tue, 20 Aug 2013 10:45:52 -0700 To: ?? <zhusy88@msn.cn> Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Question about Extract intron sequences from [gtf file] + [genome FASTA file] Message-ID: <5213AB50.1070805@bx.psu.edu> Content-Type: text/plain; charset="utf-8"; Format="flowed" Hello, There appears to be something odd with the formatting of the GTF file - the exon counts are off in the second transcript's first exon. The exon_number "1" should be "2" (remember to count reverse, is on the negative strand). But that is a side issue. There are other things that do not quite make sense, but the entire dataset was not shared. Run this again, but do the following: 1 - make sure the files are in interval format and that the column assignments are correct (click on the pencil icon) 2 - Use strand assignment or better, separate (+) and (-) stranded transcripts into two files, at the start and run the query in two workflows from there. Some GOPS tools work best this way. Also, be aware that some of these transcripts will not have intron output. For example, the first transcript in your example is a single exon transcript. Also, if you have genes with overlapping variant transcripts, these will interfere with the query (you will lose introns or fractions of introns), but I don't know how large of a dataset you are working with. If you want to pull out data per transcript, the tools in the group "Filter and Sort" can be used to subset GFF/GTF files. The last query that you ran is the ideal way to run to obtain this information in Galaxy, but the GFF to BED converter creates a BED6, not a BED12 file, and this is why the tool produced no output (see the tool form for required input). Having this tool accept GTF formatted input might be something to consider as an enhancement - I will run it by our development team and open a Trello ticket as appropriate. Another method, which may not be available to you, (from looking at the chromosome identifiers - these are not UCSC chrom IDs) -- but could help in the future or others now, is to use the UCSC Table browser. It goes something like this: 1 - Click on "display at UCSC Main" for a GTF dataset, this loads the data as a custom track, default display in assembly viewer 2 - Once in UCSC, at the top bar, pick Tools -> Table Browser 3 - In the Table Browser, change track group to "Custom Tracks" and the user track you just loaded will be there 4 - Change region = genome, then output = bed, and make sure "Send output to Galaxy" is checked, submit 5 - On the next form, you will be given a list of regions to output in the BED6 output, Introns are one of them Best, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org URL: <http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130820="" 578f6f21="" attachment-0001.html=""> Message: 3 Date: Tue, 20 Aug 2013 17:34:24 +0100 To: <galaxy-user@lists.bx.psu.edu> Subject: Re: [galaxy-user] customize tool display in the workflow Message-ID: <001201ce9dc3$21917f10$64b47d30$@qmul.ac.uk> Content-Type: text/plain; charset="us-ascii" Hi Jennifer, Many thanks for your reply. Unfortunately I am not clever to figure out how to using the existing workflow dataset renaming functions. I only know how to rename a dataset within history. Could you show me how to do this? I have attached a screen shot of my workflow. You can see that I have only managed to add annotation/notes to this step. Ideally I would like to have the step with the label of "mzidLib:PostProcessing FDR" in the graphic view. From other thread, someone mentioned to use ${method} in the label, I failed to apply this trick. Best regards! Jun Message: 3 Date: Mon, 19 Aug 2013 10:18:32 -0700 To: Jun Fan <j.fan@qmul.ac.uk> Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] customize tool display in the workflow Message-ID: <52125368.1060308@bx.psu.edu> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" Hi Jun, I asked Dannon (our workflow lead developer) and he suggested just using the existing workflow datastet renaming functions. These are in the right panel when you click on a dataset within the workflow editor (as you probably know). Inherited naming is not something that is currently being worked on, but you can always start a Trello card and see if it gathers votes or the attention of a contributor from the larger development community: http://wiki.galaxyproject.org/Support#Galaxy_Issue_Board Take care, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org URL: <http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130819="" 8dca342d="" attachment-0001.html=""> _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ End of galaxy-user Digest, Vol 86, Issue 16 ******************************************* Name: workflow renaming.png Type: image/png Size: 47319 bytes Desc: not available URL: <http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130820="" b22e6949="" attachment-0001.png=""> Message: 4 Date: Tue, 20 Aug 2013 11:34:47 -0700 To: Jun Fan <j.fan@qmul.ac.uk> Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] customize tool display in the workflow Message-ID: <5213B6C7.5030800@bx.psu.edu> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" Hi Jun, You are very close - just click on the "create" button within the "Edit Step Actions" box and it will expand, where you can then enter the new custom name. It will look something like this: The other post you are referring to is a method to name the output dataset based on the input datasets name. You can certainly try this out and see if it is useful. Hope this helps, Jen Galaxy team trick. -- Jennifer Hillman-Jackson http://galaxyproject.org URL: <http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130820="" 3406f040="" attachment-0001.html=""> Name: fdjfidfg.png Type: image/png Size: 41713 bytes Desc: not available URL: <http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130820="" 3406f040="" attachment-0001.png=""> Message: 5 Date: Wed, 21 Aug 2013 14:39:18 +0300 To: galaxy-user@bx.psu.edu Subject: [galaxy-user] Very very slow response when a class is using Galaxy from a computer room in the university Message-ID: <cagybphdue95okm5dhtewpprogcbr1tupczfxrjebdjpqgeeqdg@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear Sir/Madam, My Name is Ido Carmel, I am teaching the course titled "Advanced bioinformatics" in the Faculty of Agriculture in the Hebrew University (Israel). This year (around May), I used the Galaxy platform on the internet in a hands-on session about NGS data analysis. The session took place in one of the University computer classes with six students participating. For some reason, the Galaxy response was very very slow. It was slow when the students were signing up and also when the students were practicing very lightweight jobs that usually perform immediately such as "Fastq trimmer" or "fastq summary" statistics. Does the slow response was something seasonal or temporal? Alternatively, does the response is related to the fact that the students were in one computer room (and possibly all the queries were sent from the same proxy server)? I am teaching this course next year, do you have any advice/solution for me? Best Regards, Ido Carmel -- Ido Carmel, Dr. Yael Heifetz Lab, Robert H. Smith Faculty of Agriculture Food and Environment, The Hebrew University, POB 12, Rechovot, Israel. Tel: (+)972-8-9489222 URL: <http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130821="" 38e4989b="" attachment-0001.html=""> _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ End of galaxy-user Digest, Vol 86, Issue 17 *******************************************
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