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_ta... -Dannon