[galaxy-dev] Fix for missing included files from history export and import
Hi all, For some of the recent tools we have developed on our Galaxy instance ( http://ribogalaxy.ucc.ie), we were using the approach mentioned in the wiki for writing a single HTML output file with links to additional output files (images, csv etc.,). This is much nicer than generating multiple output files in the history panel. However, the exported histories did not contain these included files. I have now fixed this bug on our instance and have also created a pull request on Github (#417 https://github.com/galaxyproject/galaxy/pull/417 ). Implementation details: 1. Include the extra_files_path attribute on the dataset which is being exported. 2. Check if there are any files in the extra_files_path for each dataset that will be included in the archive. 3. If there are files present, create a new directory and save files to this directory. This directory will then be included in exported archive. The dataset's history ID is appended to both the directory and the dataset's name to prevent conflict with a dataset of the same name. Testing: A simple tool to test html export with included files is available at: https://testtoolshed.g2.bx.psu.edu/repos/vimalkumarvelayudhan/html_export Regards, Vimalkumar Velayudhan ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool development - Selecting a single item from input dataset.
Thanks Peter. I see how this feature would be useful, but the program I'm writing a wrapper for has an argument with values corresponding to the input files. I am using a repeat tag to maintain this order. With the multi-run option, files are selected in a random manner and added to the job queue. It is best not to display the multi-run option in this case. I see there is a TODO on this already: https://bitbucket.org/galaxy/galaxy-dist/src/a2308bdc93b897af974766b190abe019ade49e9a/lib/galaxy/tools/parameters/basic.py?at=default#cl-2084 For now, I have set allow=False but I believe this is best set at the param tag level: param type=data multirun=false / Vimal On Wed, Jan 21, 2015 at 2:26 AM, Peter Cock p.j.a.c...@googlemail.com wrote: I think this is the (relatively new) Galaxy ability to automatically run N copies of your tool given N input files, making N outputs and is related to the collections work. (This is possible if your tool takes a single input file) Peter On Tue, Jan 20, 2015 at 6:17 PM, Vimalkumar Velayudhan vi...@biotechcoder.com wrote: Hi all, I am trying to create a select box with the possibility of selecting only a single item from the input dataset (figure 1). This works fine but the option for selecting multiple files is still visible (figure 2). The multiple=false attribute has no effect. Figure: http://i.imgur.com/oJVFCoF.png I have the following in my XML. param format=tabular name=ribo_files type=data label=Select Ribo-Seq alignment file multiple=false /param Any suggestions? galaxy-dist revision 5f4c13d622b8 Regards, Vimalkumar Velayudhan ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool development - Selecting a single item from input dataset.
Hi all, I am trying to create a select box with the possibility of selecting only a single item from the input dataset (figure 1). This works fine but the option for selecting multiple files is still visible (figure 2). The multiple=false attribute has no effect. Figure: http://i.imgur.com/oJVFCoF.png I have the following in my XML. param format=tabular name=ribo_files type=data label=Select Ribo-Seq alignment file multiple=false /param Any suggestions? galaxy-dist revision 5f4c13d622b8 Regards, Vimalkumar Velayudhan ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
