I'm building a tool that needs the "display name" of a file inside the
output of the tool.

To clarify, I have a tool that merges gene expression  result from cufflinks
for many samples.  It generates a "matrix" tab-delimited file that provides
the results with genes or transcript down one axis and samples across the
other with intensity values in the cells of the matrix.

I have already built into my galaxy server the ability to carry meaningful
sample names from the original input file all the way through to the output
of the final output of the cufflinks step of my workflow (this is
functionality I've already offered up to the galaxy team to include, and can
explain at a later date).

Okay, so the problem I have is from the XML, I want to be able to pass my
command-line script both the physical file names  so the files can be
parsed, but I also want to be able to pass the script the "display name" to
use as the sample names for the columns in the file.

Is there a way using the metadata to grab this from the input?  I see that I
can do something like input.metadata.dbkey and get the database key, but I
can't find a way to do anything like input.metadata.name or
input.metadata.display_name to give me what I want.

My example XML file is below.



<tool id="cuff_exp_2_matrix" name="Merge Cufflinks Exp Files to Matrix(files
as sample names)" version="1.1.1">
  <description>merges multiple cufflinks expression output files (gene or
transcript) into a single matrix formatted file (id by sample, with
intensity values)</description>
  <command interpreter="python">
      #for $i in $inputs
      #end for
    <param name="input1" label="First file" type="data" format="tabular"
help="Need to add more files? Use controls below."/>
    <repeat name="inputs" title="Input Files">
      <param name="input" label="Add file" type="data" format="tabular" />
    <data format="tabular" name="output1" label="${tool.name} on
${on_string}: Expression matrix" />

**What it does**

This is a Jackson Laboratory custom tool for taking the output for several
runs of
cufflinks, where each run represents a sample, and merging these results
into a file
that contains a matrix of gene/transcript id by sample, with the cells of
the matrix
filled with the intensity values.  The end result is a file that is easily
into R or other tools for expression analysis.


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