October 2010 - galaxy-user - lists.galaxyproject.org

Tophat
by giovanni stefani 05 Oct '10

05 Oct '10

Hello, I am a new galaxy user, still trying to find my way around. Is there a way to run Tophat on Galaxy? Thanks Giovanni

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Undocumented tags for tool configuration
by Jelle Scholtalbers 04 Oct '10

04 Oct '10

Hey, I was looking through the bowtie_wrapper.xml to get some information about how to use the tool_data_table_conf.xml. There I also noticed in the output section the tag <actions>. Is there any information on this tag as is does seem to be used a lot? Cheers, Jelle

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How to implement the button "send query to galaxy" in UCSC Main tool
by Zhe Chen 01 Oct '10

01 Oct '10

Hi, Can u tell me how to implement the "send query to galaxy" button on page http://genome.ucsc.edu/cgi-bin/hgTables ? which is the tool in (Get Data)->(UCSC Main tool), on page 2. Thanks

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Getting data from NCBI
by Peter Young 01 Oct '10

01 Oct '10

The Get Data | Get Microbial Data tool is nice, but is limited to a subset of the older genomes among those that are currently available. It should surely be possible to get any accession directly from NCBI, but I don't see a tool to do that. The best I can do is to download a file to my computer and then upload it again to Galaxy. Am I missing something obvious? On a related point, I don't see GenBank listed as a format for conversion. Thanks Peter -- Prof J P W Young Department of Biology (Area 3) University of York Wentworth Way Heslington York YO10 5DD jpy1(a)york.ac.uk tel: +44 1904 328630(direct), 328500(department) fax: +44 1904 328505(department) http://bioltfws1.york.ac.uk/biostaff/staffdetail.php?id=jpwy http://www.york.ac.uk/depts/biol/staff/jpwy/jpwy.htm Email disclaimer: http://www.york.ac.uk/docs/disclaimer/email.htm

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Using output as parameter in workflow
by Lance Parsons 01 Oct '10

01 Oct '10

I have a user who is trying to use the output of summary statistics as input to the next step in a workflow. e.g. using "median + 2*stddev" as the threshold cutoff in the next step, which is "pileup-to-interval". Is that possible in galaxy workflow? The current workaround is to create two separate workflows and input the parameter manually, but that is less than ideal. Any suggestions would be appreciated. -- Lance Parsons - Software Developer/Data Analyst 134 Carl Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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options for history description using tool config
by Bossers, Alex 01 Oct '10

01 Oct '10

If you configure your tool using the xml config file it displays by default the tool action on data nr in the history description. This is useful but there are option to get more descriptive info in there. Default for the sequence length example: .. <outputs> <data name="output" format="tabular"/> </outputs> .. Gives: 2: Compute sequence length on data 1 This can be altered to have something like a description having the tool settings: .. <outputs> <data name="output" format="tabular" label="SEQLEN of ${query_type.value_label}" /> </outputs> .. Where you can reuse a specific selected value from the form entered by the user. Is there any documentation on this? The default tool_conf xml wiki has no specific info on this. I also noticed the use of .metadata in datasets to specify columns in that data... The specific I want to have for some of my tools is that the history line shows the tool description and the sequence name chosen. If I do: .. <outputs> <data name="output" format="tabular" label="SEQLEN of ${input1}" /> </outputs> .. I do get the sequence FILE name but with the complete not so informative path. Showing the descriptive fasta header would be even nicer.... Thanks Alex

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