Hi there

I'm trying to wrap Bioperl's bp_genbank2gff script. This script, by
default, produces an output file named the same as the basename of the
input file, with .gff added. So e.g.

bp_genbank2gff data.gbk

produces a file named data.gbk.gff.

I'm trying to use the from_work_dir attribute of the <data> tag to pick
up this file. However, if I create a tool XML like:

<tool id="Genbank2GFF3" name="Genbank to GFF3" version="1.0">
  <description>Convert Genbank format to GFF3</description>
  <command interpreter="python">
      bp_genbank2gff $genbank_filename        
      <param name="genbank_filename" type="data" format="txt">
        <label>Genbank sequence record(s)</label>
      <data format="gff3" name="gff3_filename"

I get an error from Galaxy indicating that it is trying to find a file
name $genbank_filename.gff, I.e. the ${genbank_filename} is not expanded.

Is there any way to deal with this situation? Of course the other option
is to create a tiny wrapper around bp_genbank2gff that takes an output
filename argument and does the renaming...


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:


Reply via email to