You can use $input.name to get the name you see in the history.
Unfortunately, that usually is something silly like "Samtools on data 3"....

I have changed all the labels for all the major file that are produced to provide more sensible names, usually based on the input...
An example below is how I use the original name of the BAM file when I convert it into a SAM file but just taking the prefix of the input1 and adding ".sam" at the end.

I am using the special parsing language that Galaxy is using to split the extension from the file name using the os.path.splitext function...

Untill Galaxy comes up with a better way to maintain the original file names somehow, this is your best shot...

Thon

<inputs>
    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
    <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" />
</inputs>
<outputs>
    <data format="sam" name="output1" label="#echo os.path.splitext ( str ( $input1.name ) ) [ 0 ] #.sam" />
</outputs>

On Mar 19, 2012, at 08:00 PM, diana michelle magbanua <dmdrmagbanua@gmail.com> wrote:

Hi there,

I am new to Galaxy and I've just recently learned how to integrate a Perl script to it. Now, my code uses the input file's name as a header for a column in the output. When I ran it in Galaxy, I did get the filename, but it's the one ending in .dat (actually, I got the entire path of the file). I was wondering if it's possible to retain the original name of the file (or retrieve the name of the input dataset) and use it in the output file. I can't think of a Perl script for this yet, for my scripting's a bit rusty (I just started learning Perl last month). I've already checked the FAQs page, the wiki and the mailing list, but I did not get any useful hints.

I hope my writing made sense. Thank you for your time!

- Diana
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