Just a follow up here ... if the <command> tag needs to list all output files, but the tool itself does not specify output files on the command line, does that mean I need to write a wrapper for my tool that accepts each output file as a command-line parameter? Currently I've tried specifying all of the output files on the <command> line, where each variable corresponds to a <data> line under outputs, but then SOAPaligner/soap2 tries to read those non-existent files as FASTA files. As a more general question, is there a way to see the exact command(s) that Galaxy is dispatching on my behalf when I execute a tool? I checked paster.log but it wasn't there. It seems like that would be a great debugging feature. Branden On Aug 17, 2010, at 10:06 AM, Hans-Rudolf Hotz wrote:
Hi Branden
Hello, I'm very new to Galaxy, and trying to use SOAPaligner/soap2 as a test integration case.
soap2 includes two executables, 2bwt-builder and soap. 2bwt-builder takes a FASTA files and generates a set of 13 different index files, which soap needs in order to do it's alignment.
I have started by just creating the tool XML configuration for 2bwt-builder. The configuration follows:
<tool id="2bwt-builder" name="2bwt-Builder"> <description>build index files for the SOAPaligner/soap2</description> <command>2bwt-builder $input</command>
the "command line" needs all output files listed, see: http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial
However, in your case: Do you really want to make an extra tool for the indexing step? Wouldn't it make more sense to have the indices pre-built for some genomes?
Your soap galaxy tool can then re-use the indices again and again. This is also much more space efficient, as all the user share the same index files.
Regards, Hans
<inputs> <param type="data" format="fasta" name="input" label="Source file"/> </inputs>
<outputs> <data format="tabular" name=".amb Index File"/> <data format="tabular" name=".ann Index File"/> <data format="tabular" name=".bwt Index File"/> <data format="tabular" name=".fmv Index File"/> <data format="tabular" name=".hot Index File"/> <data format="tabular" name=".lkt Index File"/> <data format="tabular" name=".pac Index File"/> <data format="tabular" name=".rev.bwt Index File"/> <data format="tabular" name=".rev.fmv Index File"/> <data format="tabular" name=".rev.lkt Index File"/> <data format="tabular" name=".rev.pac Index File"/> <data format="tabular" name=".sa Index File"/> <data format="tabular" name=".sai Index File"/> </outputs> </tool>
I've used the tabular data type for the output files, which I'm not sure is correct. When the script runs, it generates 13 output files in my history, but they are all empty according to galaxy. When I look at galaxy_dist/database/files/.../, the output files have been generated correctly and are non-empty.
Where am I going wrong? Thank you in advance for any advice.
-- Branden Timm System Administrator Great Lakes Bioenergy Research Center University of Wisconsin btimm@glbrc.wisc.edu _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev