Naming output file according to input file

Question: Naming output file according to input file

2.8 years ago by

Rob • 50

France

Rob • 50 wrote:

Hello,

I currently develop a galaxy tool and I want to remove the extension from my input file. For example, if my input file is "myfile.bam", I want to return a file named "myfile.something".

I would like to do something like that :

<data name="output1" label="${input}.something"/>

But I don't know how to remove the .bam extension, just how to add other things after it.. How can I do that ?

tool dev galaxy • 1.5k views

ADD COMMENT • link •

modified 6 months ago by Thon deBoer • 20 • written 2.8 years ago by Rob • 50

If ${input} is a data parameter it will never have the .bam ending. It will have a .dat ending. Just set the format="sam" and Galaxy and all users will know it's a SAM file.

ADD REPLY • link written 2.8 years ago by Bjoern Gruening ♦ 5.1k

Hi, thanks for your answer.

That the point. (you're right my example was wrong, sorry, I will correct that, but it show what I want to do) but by input file I mean the user file, witch is a .bam. And I want to rename my output file by myself, cause in fact the soft doesn't product an extension recognize by Galaxy, and so I can't use the format attribute.

So what I want is to take the input file name (smth.bam) remove the .bam extension and add something other (.aaa or what you want) for the output.

(I have updated my post a little bit cause it wasn't really explicit)

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by Rob • 50

The true command seem to be :

<data name="output1" label="${input1.name}.something">

It return myInputFile.bam.something, but it's not what I want, do you have an idea for remove the .bam ?

ADD REPLY • link written 2.8 years ago by Rob • 50

The data tag takes a format attribute. Then it doesn't matter what file extension the results happen to have.

ADD REPLY • link written 2.8 years ago by Devon Ryan • 1.9k

Okay, but the format attribute doesn't modify the output file name.

So I guess it's impossible to work on the name itself. Since my input file format is not recognized by Galaxy, I am then condemned to keep this extension in my output file name..

Thanks for your answers.

ADD REPLY • link written 2.8 years ago by Rob • 50

6 months ago by

Thon deBoer • 20

Thon deBoer • 20 wrote:

It is possible to use python code in the labels, so this should work:

<data name="output1" label="${os.path.splitext(os.path.basename($input1.name))[0]}.something">

You can't use the { } for the $input1.name, but you DO need it for the python code, but this will do what you want.

it will name your output file "myInputFile.something".

Adopted from https://stackoverflow.com/questions/678236/how-to-get-the-filename-without-the-extension-from-a-path-in-python

ADD COMMENT • link written 6 months ago by Thon deBoer • 20

Actually..you often don't need the os.path.basename part. That is only needed if you ever pass it a full path (but it doesn't hurt and I just always use it)

ADD REPLY • link written 6 months ago by Thon deBoer • 20

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