That did it! Silly mistake - thanks so much!!

-----Original Message-----
From: Dannon Baker [mailto:dannonba...@me.com] 
Sent: Wednesday, March 28, 2012 2:21 PM
To: Brami, Daniel
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] toolrunner / xml parse

>     <data format="fastqsanger" name="readleft" type="data" label="Left fastq 
> reads FASTQ files" ftype="fastqsanger" />
>     <data format="fastqsanger" name="readright" type="data" label="Right 
> fastq reads FASTQ files" ftype="fastqsanger" />

These inputs should be defined using the <param> tag, and not the <data> tag.   
Here's the wiki page with more details: 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cparam.3E_tag_set

-Dannon

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