Sarah: I've had trouble before with invalid xml files (in your case test.xml) I don't see an obvious problem with your file, but I've never tried such a minimal file.
Have a look at galaxy's log during startup to see if it tells you what it does not like about the file. Brad -- Brad Langhorst New England Biolabs langho...@neb.com On 2/7/12 6:32 AM, "Sarah Maman" <sarah.ma...@toulouse.inra.fr> wrote: >Hello, > >I managed to add a new tool coded in bash but I am having some >difficulty adding a tool coded in python. > >Here are the contents of the test files: >* Content of test.xml file in galaxy/galaxy-dist/tools/test/test.xml : ><tool id="test" name="Test name"> > <description>Test description</description> > <command interpreter="python">test.py</command> ></tool> > >* Content of test.py file in galaxy/galaxy-dist/tools/test/test.py : >#!/usr/bin/python > >import os > >for param in os.environ.keys(): > print "%20s %s" % (param,os.environ[param]) > >* Content of tool_conf_xml file in galaxy/galaxy-dist/ : ><?xml version="1.0"?> ><toolbox> > <section name="Get Data" id="getext"> > <tool file="test/test.xml" /> > <tool file="uploadFile/uploadFile.xml" /> > <tool file="data_source/upload.xml"/> > <tool file="data_source/ucsc_tablebrowser.xml" /> > <tool file="data_source/ucsc_tablebrowser_test.xml" />...... > >Could you, please, explain me why the new tool "test" isn't avalaible in >Tools/Get Data windows (on the left, before uploadFile and upload tools ) >? > >Thanks in advance, >Sarah > >___________________________________________________________ >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/ ___________________________________________________________ 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/
