Dear Thondeboer, Thank you very much for your help. I have tried your method. It woks well.
Best Regards, HU Yingwei 2012/2/25 <thondeb...@me.com> > 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 ( $inputFile.name ) ) [ 0 ] > #-ReHead.bam" > > That will extract the basename of the file (The stuff before a period) and > attached "-ReHead.bam" to the original input file name ($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... > > Thon > > > 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 > "dist-path/database/files/000/dataset_12.dat". > 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: > > http://lists.bx.psu.edu/ > > >
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