[galaxy-user] viewing data live while tool is running

2013-07-30 Thread Ketan Maheshwari
Hi, I am a relatively new Galaxy user. I am wondering if there is an example of a tool which allows users to view at the stdout/err of a tool live while it is still running to get a sense of progress it is making. The tools I have had experience with so far will save the stdout/err or an

[galaxy-user] tool within a tool

2013-08-21 Thread Ketan Maheshwari
Hi, I am wondering if it is possible in Galaxy to design a tool whose sole purpose is to run other tools. This is motivated by our desire to enhance execution capabilities of existing tools via a generic tool which acts as a wrapper. Thanks, -- Ketan

[galaxy-user] special character $ gets converted to X in tool

2014-01-31 Thread Ketan Maheshwari
Hi, In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable. Is there a way to work around this

Re: [galaxy-user] special character $ gets converted to X in tool

2014-01-31 Thread Ketan Maheshwari
Thanks! Just wanted to report that \$ does not work; \ adds one more X. On Fri, Jan 31, 2014 at 11:29 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hi, In a test tool that I am working on, I need

Re: [galaxy-user] special character $ gets converted to X in tool

2014-02-01 Thread Ketan Maheshwari
Thank you. It worked and the sanitizer tag sounds very useful. On Sat, Feb 1, 2014 at 4:14 AM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Ketan! it sounds like your input is sanitized. You can disable it for your whole wrapper or you can write a special sanitizer for your input field:

[galaxy-user] remove versions of tool

2014-02-01 Thread Ketan Maheshwari
Hi, I renamed my tool name in tool name= but when I restart Galaxy server, I see a dropdown in front of the tool title with two versions with same value. When I select one it gives current name and when selecting other it gives the older name of the tool. My intention here was to rename the tool

Re: [galaxy-user] remove versions of tool

2014-02-01 Thread Ketan Maheshwari
Hi Bjoern, This is a tool I am developing. In Galaxy admin, I could not find any option to manage tools and versions. In my tools directory, there is just one tool xml file for this tool. Thanks, Ketan On Sat, Feb 1, 2014 at 6:40 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Ketan,