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Question: How to define multiple accepted data input formats for custom tool in the XML file?
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gravatar for LF
3.5 years ago by
LF • 10
United States
LF • 10 wrote:

Hi all,

I am working on implementing a custom tool for a galaxy server and was wondering about the best way to allow for both fastq and fastq.gz input format.

For example, my XML <inputs> tag contains the following <param> tag right now:

<param type="data" name="R1" format="fastq" label="FWD reads (R1)"/>

However, the tool will also accept fastq.gz input data -- how do I make galaxy aware of this?

Thanks for any help!
datatype xml specification custom tool • 1.4k views
ADD COMMENT • link •
modified 3.5 years ago by Bjoern Gruening ♦ 5.1k • written 3.5 years ago by LF • 10
1
gravatar for Bjoern Gruening
3.5 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

The problem is that Galaxy will automatically unpack your fastq file during upload. So there is actually no fastq.gz file in Galaxy and no datatype for it. If there would be a datatype you could simply do `format="fastq,fastqsanger,fastq.gz"`.

Ciao,

Bjoern
ADD COMMENT • link written 3.5 years ago by Bjoern Gruening ♦ 5.1k

Great, thanks for the help!

ADD REPLY • link written 3.5 years ago by LF • 10
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