I am getting an error upon my local Galaxy startup which I suspect is causing an invalid tool runner entry in my left hand menu (my tool url is: http://localhost:8081/tool_runner/index instead of http://localhost:8081/tool_runner?tool_id=FLASHforFASTQ)

Here is the error I get:

galaxy.tools DEBUG 2012-03-28 13:48:28,658 Loading section: MyTools

galaxy.tools DEBUG 2012-03-28 13:48:28,665 Loaded tool: sam_to_bam_QT 0.0.1

galaxy.tools DEBUG 2012-03-28 13:48:28,671 Loaded tool: BAMtoFASTQ 0.01

galaxy.tools.test DEBUG 2012-03-28 13:48:28,677 Error in add_param for readleft: Unable to determine parameter type of test input 'readleft'. Ensure that the parameter exists and that any container groups are defined first.

galaxy.tools.test DEBUG 2012-03-28 13:48:28,677 Error in add_param for readright: Unable to determine parameter type of test input 'readright'. Ensure that the parameter exists and that any container groups are defined first.

galaxy.tools DEBUG 2012-03-28 13:48:28,678 Loaded tool: FLASHFASTQ 0.01

Here is the xml for my tool:

<tool id="FLASHFASTQ" name="FLASH Overlap for FASTQ" version="0.01">

  <description>Finds overlaps between paired fastq files or fills the insert with N's</description>

  <command interpreter="python">

    FLASHforFASTQ.py

      --readleft=$readleft

      --readright=$readright

      --output=$output1

  </command>

  <inputs>

    <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" />

  </inputs>

  <outputs>

    <param format="fasta" name="output1" type="data" label="Overlap sequences in FASTA format"/>

  </outputs>

  <tests>

    <test>

      <!--

      FLASH to FASTQ conversion command:

      /bioinformatics/asm/bio_bin/Galaxy/galaxy-dist/tools/mytools/FLASHforFASTQ.py -lr -rr -output1

      -->

      <param name="readleft" value="quick-taxa.r1.fastq" type="data" ftype="fastqsanger" />

      <param name="readright" value="quick-taxa.r2.fastq" type="data" ftype="fastqsanger" />

      <output name="output1" file="quick-taxa.fasta" ftype="fasta" />

    </test>

  </tests>

  <help>

**What it does**

This tool uses a modifed version of the FLASH overlapper to overlap paired end reads together and outputs the the resulting sequence in FASTA format

  </help>

</tool>

What’s the problem?!?!

Daniel Brami
Synthetic Genomics, Inc.
Senior Research Associate, Bioinformatics
11149 North Torrey Pines Road
La Jolla, California  92037
Phone: 858.433.2230
Fax: 858.754.2988
DBrami@SyntheticGenomics.com
www.SyntheticGenomics.com