Question: How to define multiple accepted data input formats for custom tool in the XML file?
0
gravatar for LF
3.1 years ago by
LF10
United States
LF10 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!

ADD COMMENTlink modified 3.1 years ago by Bjoern Gruening5.1k • written 3.1 years ago by LF10
1
gravatar for Bjoern Gruening
3.1 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k 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 COMMENTlink written 3.1 years ago by Bjoern Gruening5.1k

Great, thanks for the help!

ADD REPLYlink written 3.1 years ago by LF10
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