Thank you very much for your help.
I have tried your method. It woks well.
> The field $input.name will give you the visible name from the history.
> But those are usually not very useful,since they usually are something
> like "Intersect on Data 23 and Data 24"
> I have began to change all the labels for most of the tools to something
> more useful such that it is clear from the label what the original file was
> that you used. Specifically for FASTQ files and mapping etc.
> So when I start with a fastq file called "165_1_ACGTAG.fastq" and I run
> BWA, I get "165_1_ACGTAG-bwa.sam".
> Then when I changed that to BAM that, I get "165_1_ACGTAG-bwa.bam" and
> when I change the header, I get something like
> "165_1_ACGTAG-bwa-ReHead.bam" etc.
> The trick I use for that is something like this:
> label="#echo os.path.splitext ( str ( $paired.input1.name ) ) [ 0 ]
> #-PE-bwa.sam" for BWA for instance
> Later, in a different tool I use:
> label="#echo os.path.splitext ( str ( $inputFile.name ) ) [ 0 ]
> That will extract the basename of the file (The stuff before a period) and
> attached "-ReHead.bam" to the original input file name ($inputFile.name).
> This way it becomes much clearer what the file contains and what its
> history is.
> It is using the Cheetah syntax (Cheetah Users'
> Guide<http://www.cheetahtemplate.org/docs/users_guide_html/>) to extract and
> reformat the strings. Everything between the two hashmarks
> is treated as CHEETAH code.
> It is not a trivial task to change all the labels and sometimes you have
> to fudge a little (in the case of multiple input files for instance...Then
> I just choose the first...Also it becomes more tricky when there are some
> conditional statements (such as in BWA)...>Then you sometimes have to
> duplicate the code to make it work...But it is possible...
> I have attached a few of my .xml file for the most popular tools...Hope
> they help...
> On Feb 24, 2012, at 07:05 AM, Yingwei HU <husi...@gmail.com> wrote:
> Dear all,
> May I ask how to get the raw file name of the uploaded dataset?
> The value of $input assigned from <param name="input" type="data"
> format="xml"> is a file name like
> However, I really need to get the raw file name like "abc.xml" which seems
> to be stored as attribute "name" of the uploaded dataset.
> How can I get the raw file name?
> Please help me. Thank you very much.
> Yingwei HU
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: