I figured it out!
The mistake I was making was assuming that I needed to use the "metadata"
attribute. I found in the "Data" base class that there is a display_name
method.
So instead in my xml I just used the syntax $input.display_name and I got
exactly what I was looking for.
Are things like this documented somewhere? I couldn't find it in the wiki,
and it took digging into the code and quite a bit of trial and error to
figure it out.
Thanks,
Dave
On 6/16/11 9:08 AM, "Dave Walton" <dave.wal...@jax.org> wrote:
> 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.
>
> Thanks,
>
> Dave
>
> <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">
> cuff_exp_2_matrix_new.py
> $input1.metadata.display_name
> $input1
> $output1
> #for $i in $inputs
> ${i.input.metadata.display_name}
> ${i.input}
> #end for
> </command>
> <inputs>
> <param name="input1" label="First file" type="data" format="tabular"
> help="Need to add more files? Use controls below."/>
> <repeat name="inputs" title="Input Files">
> <param name="input" label="Add file" type="data" format="tabular" />
> </repeat>
> </inputs>
> <outputs>
> <data format="tabular" name="output1" label="${tool.name} on
> ${on_string}: Expression matrix" />
> </outputs>
> <help>
>
> **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
> imported
> into R or other tools for expression analysis.
>
> </help>
> </tool>
>
>
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