Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents
Hi Greg, Thanks for the tips. A validator would indeed be great as I made the changes you suggested but still it did not solve the issue (the tool still does not appear - so probably yet another mistake is there...). Regards, Pieter. From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: donderdag 24 oktober 2013 17:29 To: Lukasse, Pieter Cc: 'Peter Cock'; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents Hello Pieter, There are 2 different issues in 2 of your xml files that make them invalid XML. 1. In your tool_dependencies.xml file, you need to close the version string attribute in the package tag. So the following line with the problem: package name=xtandem version=12.10011 is fixed when it looks like this: package name=xtandem version=12.10011 2. In your mass comb_dbsearch_xtandem.xml file, the comment outside of the /tool tag on the last line problematic. /tool !-- NB: edit /etc/profile and add the xtandem bin folder to PATH -- The above XML results in the XML document being parsed such that the XML root is the comment itself. If you move the comment line insideo of the tool tag set, all is well: !-- NB: edit /etc/profile and add the xtandem bin folder to PATH -- /tool Unfortunartely, it is difficult to render meaningful messages for invalid XML like this as the XMNL parser does not provide much of anything meaningful that can be passed on in the UI. At some point I may find the chance to incorporate a validator, but just don't currently have the time. Greg Von Kuster On Oct 24, 2013, at 10:46 AM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: Hi Peter, I've added the package to the test toolshed now as well, but there the revision is not seen in the metadata (see screenshot). What is needed to get this repository active? Is this still the reset metadata (is this a bug or by design)? Thanks for your help! image001.jpg Regards, Pieter. -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.comhttp://googlemail.com] Sent: donderdag 24 oktober 2013 13:27 To: Lukasse, Pieter Cc: Greg Von Kuster (g...@bx.psu.edumailto:g...@bx.psu.edu); galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents On Thu, Oct 24, 2013 at 12:09 PM, Lukasse, Pieter pieter.luka...@wur.nlmailto:pieter.luka...@wur.nl wrote: Hi , I have a toolshed repository where I expect 5 tools to appear in the Contents of this repository section but one of them fails to appear in the list (see screenshot). Where can I find out what is going wrong? Thanks, Pieter. Hi Pieter, The first thing to confirm is if the missing tool a valid XML file? Next, does it work in your Galaxy instance (if installed manually). Now if this problem is only in the Tool Shed, which toolshed is it in? Your own local tool shed, the main Penn State public Tool Shed, the Penn State Test Tool Shed, or somewhere else? If it is your own tool shed, you should be able to look at its logging for clues. If it is a public tool shed, please share the URL for the repository. Regards, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents
On Fri, Oct 25, 2013 at 2:26 PM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Greg, Thanks for the tips. A validator would indeed be great as I made the changes you suggested but still it did not solve the issue (the tool still does not appear – so probably yet another mistake is there...). Try any generic XML validator - it won't know about the special Galaxy tags etc, but will still catch the majority of stupid mistakes. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents
Kind of assuming Greg did this yesterday when he replied with only two problemsbut you are right, I can check the XML correctness locally (although this does not solve the fundamental problem). Regards, Pieter. -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: vrijdag 25 oktober 2013 15:49 To: Lukasse, Pieter Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents On Fri, Oct 25, 2013 at 2:26 PM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Greg, Thanks for the tips. A validator would indeed be great as I made the changes you suggested but still it did not solve the issue (the tool still does not appear - so probably yet another mistake is there...). Try any generic XML validator - it won't know about the special Galaxy tags etc, but will still catch the majority of stupid mistakes. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents
Hi Pieter, Perhaps I'm misunderstanding this issue. Can you clarify the problem? Thanks, Greg Von kuster On Oct 25, 2013, at 9:53 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Kind of assuming Greg did this yesterday when he replied with only two problemsbut you are right, I can check the XML correctness locally (although this does not solve the fundamental problem). Regards, Pieter. -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: vrijdag 25 oktober 2013 15:49 To: Lukasse, Pieter Cc: Greg Von Kuster; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents On Fri, Oct 25, 2013 at 2:26 PM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Greg, Thanks for the tips. A validator would indeed be great as I made the changes you suggested but still it did not solve the issue (the tool still does not appear - so probably yet another mistake is there...). Try any generic XML validator - it won't know about the special Galaxy tags etc, but will still catch the majority of stupid mistakes. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] pass regular expression
Hi all, I am trying to develop a tool which allows the user to use regular expression to only keep the lines matching the given pattern in the output. There are many special characters, e.g. \ in \d. In the perl script the wrapper invokes, the regular expression is printed as Xd+ for the regular expression \d+. My question is how to pass these special characters including \, (, ), ^ etc. correctly into the perl script. Best regards! Jun ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] pass regular expression
Hi, Jun. The inbuilt parameter sanitizer can be controlled - see http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set The valid sub-tag allows precise control and you can specify eg string.printable if you want ANY printable character in your parameter Here's an example from the Tool Factory: param name=tool_name type=text value=My dynamic script label=New tool ID and title for outputs size=60 help=This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with$ sanitizer invalid_char= valid initial=string.letters,string.digits/ /sanitizer /param I hope this helps? On Sat, Oct 26, 2013 at 11:43 AM, Jun Fan j@qmul.ac.uk wrote: Hi all, ** ** I am trying to develop a tool which allows the user to use regular expression to only keep the lines matching the given pattern in the output. There are many special characters, e.g. \ in \d. In the perl script the wrapper invokes, the regular expression is printed as Xd+ for the regular expression \d+. My question is how to pass these special characters including \, (, ), ^ etc. correctly into the perl script. ** ** Best regards! Jun ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
