[galaxy-dev] toolrunner / xml parse

2012-03-28 Thread Brami, Daniel 
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
  descriptionFinds 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.commailto:dbr...@syntheticgenomics.com
www.SyntheticGenomics.comhttp://www.syntheticgenomics.com/

___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] toolrunner / xml parse

2012-03-28 Thread Brami, Daniel 
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

___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/