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
dbr...@syntheticgenomics.com<mailto:dbr...@syntheticgenomics.com>
www.SyntheticGenomics.com<http://www.syntheticgenomics.com/>

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