Hello,
Sorry if this is a double post, I tried to send a message earlier
today and accidentally sent it incomplete.
I am working on integrating SOAPaligner/soap2 into Galaxy. soap2
includes two executables, 2bwt-builder which takes a FASTA file and
generates 13 index files, and soap which uses these index files for
alignment.
Here is my configuration for 2bwt-builder:
<tool id="2bwt-builder" name="2bwt-Builder">
<description>build index files for soap</description>
<command>2bwt-builder $input</command>
<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>
The tool runs in Galaxy, but when it finishes it puts 13 empty data
files in my history. I can see in database/files/.../ that the output
of 2bwt-builder is correct and the indexes are non-empty files. I'm
guessing that tabular may be the wrong format for these output files,
but I'm not really sure what other datatype they would be. Perhaps I
need to define my own. Where am I going wrong?
Cheers
--
Branden Timm
System Administrator
Great Lakes Bioenergy Research Center
University of Wisconsin
btimm(a)glbrc.wisc.edu
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