User: Bob

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Bob0
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Posts by Bob

<prev • 18 results • page 1 of 2 • next >
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Answer: A: Dynamic Tool Parameter Lists based on an Input File
... Maybe a concrete example would help? We start with a JSON file as input (typically by uploading). Here's a simple example holding values of length, width, and height: { "parameters": [ { "par_name": "length", "par_expression": "25", ...
written 13 months ago by Bob0
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Answer: A: Named Command Line Argument Conventions
... Thanks for the tip. I looked at some of the documentation and they appear to be using the common Linux/UNIX/GNU syntax: > bamCoverage --bam a.bam -o a.SeqDepthNorm.bw > --binSize 10 > --normalizeTo1x 2150570000 > --ignoreForNormalization chrX > --extendReads > &g ...
written 13 months ago by Bob0
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Dynamic Tool Parameter Lists based on an Input File
... What is the best way (or any way) to generate dynamic Galaxy tool fields based on data inside a selected data set file? Part of our pipeline involves a JSON file containing a number of name/value pairs that we call our "model parameters". The name/value pairs are dynamically defined outside of Gala ...
galaxy written 13 months ago by Bob0
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Named Command Line Argument Conventions
... Are there any Galaxy community standards for identifying command line arguments by name? We are adapting a suite of tools to work in Galaxy and we're writing the "glue" code that will pass parameters from the Galaxy GUI to our tools. All of the examples I've seen so far show positional parameters ...
wrapper galaxy development tool written 13 months ago by Bob0
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Comment: C: Galaxy 101 Tutorial
... Training materials almost always lag ongoing development. That's hard to avoid. The Galaxy 101 tutorial suffered from the additional changes made to the data base - which weren't needed for the tutorial itself. It's great to use real active databases, but having one that you control internally has ...
written 14 months ago by Bob0
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Answer: A: Galaxy 101 Tutorial
... Comment: For someone getting started with a "101" tutorial, it's really helpful if everything is exactly as it's advertised to be. Even little things like the difference between an item that says "variations and repeats" and two different items named "variations" and "repeats" causes a degree of un ...
written 14 months ago by Bob0
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Answer: A: Just getting started with Galaxy 101 Tutorial
... Thanks Mo. For anyone following along, I found the newly added "Join" function under the "Get Data" menu (on the left side). With that tool, I was able to complete the Galaxy 101-1 tutorial. With the best of intentions, let me observe that the tutorial (especially with a "101" name) could use som ...
written 14 months ago by Bob0
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Comment: C: Just getting started with Galaxy 101 Tutorial
... So the option to: "Join two Datasets side by side on a specified field" is NOT the one to use? I didn't see any instructions about installing different tools. "Galaxy 101" might have been a mild misnomer. ---------- I'm adding to this post since the anti-spam feature is limiting me to 5 ...
written 14 months ago by Bob0
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Comment: C: Just getting started with Galaxy 101 Tutorial
... In my version, the left panel shows: - Get Data - Send Data - Collection Operations - Text Manipulation - Filter and Sort - Join, Subtract and Group - Convert Formats - Extract Features - Fetch Sequences - Fetch Alignments - Statistics - Graph/Display Data - Workflows - All workflows ...
written 14 months ago by Bob0
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Answer: A: Just getting started with Galaxy 101 Tutorial
... Note that the "Join" page above is different from the one in the version of Galaxy that I have. Mine shows: Join two Datasets side by side on a specified field (Galaxy Version 2.0.2) Join 1. Exons using column Column: 1 with 2: SNPs and column Column ...
written 14 months ago by Bob0

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