I have a new local install of Galaxy on my own server and I'm trying to define a new tool for a command line program. I'm following the Add Tool Tutorial and I'm at the point where I need to let my galaxy installation know about my new tool. in galaxy/config I copied tool_conf.xml.sample to tool_conf.xml. Then I edited this file and added the following block:
<section name="MyTools" id="mTools"> <tool file="hgtfinder/hgtfinder.xml" /> </section> </toolbox>
my tool and xml file are in galaxy/tools/hgtfinder. When I start up galaxy I don't see my new tool in the list. What did I do wrong?
Here is my hgtfinder.xml:
<tool id="hgt_finder" name="HGT Finder" version="0.1.0"> <description>Find horizontally transferred genes</description> <command >hgt-finder/HGTFinder -d $nrBlast -s $selfBlast -t $taxId -o HGT -r 0.5</command> <inputs> <param format="tabular" name="nrBlast" type="data" label="BLAST to nr database"/> <param format="tabular" name="selfBlast" type="data" label="Self BLAST"/> <param name="taxId" type="integer" label="NCBI Taxonomy ID"/> </inputs> <outputs> <data format="tabular" name="output" /> </outputs> <help> This tool finds HGT. </help> </tool>