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 $genbank_filename        
  </command>
  <inputs>
      <param name="genbank_filename" type="data" format="txt">
        <label>Genbank sequence record(s)</label>
      </param>
  </inputs>
  <outputs>
      <data format="gff3" name="gff3_filename"
from_work_dir="${genbank_filename}.gff">
      </data>
  </outputs>
  <help>
  </help>
</tool>

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...

Peter

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