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Tools with auto_format='true' connectable in workflow editor #2144

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merged 1 commit into from Apr 15, 2016

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@yhoogstrate
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commented Apr 13, 2016

Dear Galaxy team,

I have created a (Get Data) tool that obtains data from a database, but a priori the data type is unknown. I found out that using the XML tag <outputs><data ... auto_format="true" /></outputs>, galaxy is able to detect the data type using its internal sniffing system, by setting the data the in the background to _sniff_. This works perfectly and I am really happy about it :).

When I wanted to use the tool in a workflow, connected to a tool that expects FASTQ data, it turned out that they couldn't be connected because the one data type is _sniff_ and the other is fastq. To figure out whether galaxy has internal constraints that really prevent this, I simply downloaded the GA file, changed the links, and uploaded the GA file gain. Fortunately, the workflow worked, so I knew the issue was only a limitation within the GUI / javascript code.

I tracked down the location of this constraint, modified it and now the sniffable output can be connected to any other tool just from the GUI. I hope you like the change. The two files within ./static are compiled by grunt.

all best,

Youri

@galaxybot galaxybot added the triage label Apr 13, 2016

@galaxybot galaxybot added this to the 16.07 milestone Apr 13, 2016

@nsoranzo

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commented Apr 13, 2016

@yhoogstrate FYI, the recommended way to rebuild the files in static/ is to run make client (not sure that would change anything for this PR).

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commented Apr 15, 2016

Excellent - thanks!

@jmchilton jmchilton merged commit 5a747bd into galaxyproject:dev Apr 15, 2016

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@yhoogstrate yhoogstrate deleted the yhoogstrate:galaxy_workflow_autosniff branch Apr 15, 2016

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