Hi all,
I just uploaded a (Sanger) FASTQ file without specifying the format.
Galaxy therefore treats it as "fastq". Some tools are happy to take this
as input, but not the fastq_to_tabular converter. Please consider applying
the following trivial patch:
--- a/tools/fastq/fastq_to_tabular.xml Wed Nov 17 16:24:12 2010 -0500
+++ b/tools/fastq/fastq_to_tabular.xml Mon Dec 13 16:52:51 2010 +0000
@@ -2,7 +2,7 @@
<description>converter</description>
<command interpreter="python">fastq_to_tabular.py '$input_file'
'$output_file' '${input_file.extension[len( 'fastq' ):]}'</command>
<inputs>
- <param name="input_file" type="data"
format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa"
label="FASTQ file to convert" />
+ <param name="input_file" type="data"
format="fastq,fastqsanger,fastqcssanger,fastqillumina,fastqsolexa"
label="FASTQ file to convert" />
</inputs>
<outputs>
<data name="output_file" format="tabular" />
Thanks,
Peter