Hello Janaki,

Thanks for clarifying that you have installed your tools from a Tool Shed.  In 
this case, functional tests do not use Galaxy's tool_conf.xml.sample, so 
changing it will make no difference.  For information about running functional 
tests on tools installed from the Tool Shed, see: 
https://wiki.galaxyproject.org/TestingInstalledTools

Basically, you'll be doing the following.  The functional test framework is not 
currently set up to test a specific installed tool using a -id flag.  You'll 
have to use just the -installed flagg which will end up testing all installed 
tools.

export GALAXY_TOOL_DEPENDENCY_DIR=tool_dependencies;  sh 
run_functional_tests.sh -installed

Greg Von Kuster

On Mar 27, 2014, at 8:58 AM, Janaki Rama Rao Gollapudi 
<janakiram.gollap...@india.semanticbits.com> wrote:

> Hi,
> 
> Thanks for reply. I composed a details email for better clarity. 
> 
> when run grep command in galaxy home folder ( ./run_functional_tests.sh -list 
> | grep barcode-parse), I got no results. 
> What I did was:        
> Implemented a custom tool (It has one python script and tool definition file. 
> These files are located in ../tools/Mytools/customToolName/)
> Then run the ToolShed in my local which is running on port 9009 (I have)
> Created a new repository in the ToolShed (which is running on 9009) and 
> uploaded .py and .xml files in to it
> Now I run the galaxy (running on port 8080) and browse the my custom tool 
> from my local galaxy and install the custom tool successfully
> And "shed_tool_conf.xml" file updated with new section: 
> <section id="mTools" name="MyTools" version="">
>   <tool 
> file="xxx.xx.x.xx/repos/janakiram-t1/barcode_parse_1/b6a60d02b1a2/barcode_parse_1/barcode-
>       parse.xml" 
> guid="xxx.xx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0">
>       <tool_shed>xxx.xxx.x.xx:9009</tool_shed>
>         <repository_name>barcode_parse_1</repository_name>
>         <repository_owner>janakiram-t1</repository_owner>
>         
> <installed_changeset_revision>b6a60d02b1a2</installed_changeset_revision>
>         
> <id>xxx.xxx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0</id>
>         <version>1.0.0</version>
>     </tool>
> </section>
> 
> My tool definition  file look likes below:
> <tool id="barcode-parse" name="Barcode parse">
>     <description>some description</description>    
>     <command interpreter="python">barcode-parse.py $input1 $input2 
> $output</command>
>     <inputs>
>         <param format="input" name="input1" type="text" size="50" 
> label="barcode" help="Enter barcode">
>                        <validator type="empty_field" message="please enter 
> barcode"/>
>               </param>
>               <param format="input" name="input2" type="text" size="50" 
> label="Expected format" help="Enter format to parse barcode">
>                       <validator type="empty_field" message="please enter 
> expected format barcode"/> 
>               </param>
>     </inputs>
>     <outputs>
>         <data format="txt" name="output" />  
>     </outputs>
>     <tests>
>        <test>
>          <param name="input1" 
> value="test-01-sample-test-02-sampl1-test-03-sample3"/>
>          <param name="input2" value="name-id"/>
>          <output name="output" file="barcode-parse.txt"/>
>        </test>
>     </tests>
>     <help>
>        Parse the barcode into expected format
>     </help>
> </tool>
> As galaxy using  tool_conf.xml.sample, this file has no section for my custom 
> tool. I have added a section manually like below:
> 
>  <section name="MyTools" id="mTools">
>          <tool file="myTools/barcode-parse/barcode-parse.xml" />
>   </section>
> 
> Then my tool id found when I run the grep command. After that Then I run the 
> below command to run the test cases:
> 
> sh run_functional_tests.sh -id barcode-parse
> 
> But I got below out put (from the run_functional_tests.html)
> 
> 
> AttributeError: 'module' object has no attribute 
> 'test_toolbox:TestForTool_barcode-parse'
> 
> Am I doing anything wrong.
> 
> Thanks,
> JanakiRam
> 
> 
> On Thu, Mar 27, 2014 at 6:16 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> As Janaki replied below, see: 
> http://wiki.galaxyproject.org/Admin/RunningTests?action=show&redirect=Admin%2FRunning+Tests
> 
> On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi 
> <janakiram.gollap...@india.semanticbits.com> wrote:
> 
>> Hi,
>> 
>> I have added tests to tool dependency xml, but how should I run these tests, 
>> can you please help me to run test cases. 
>> 
>> .....................
>>  <tests>
>>        <test>
>>          <param name="input1" value="some string"/>
>>          <param name="input2" value="expected format"/>
>>          <output name="output" file="output.txt"/>
>>        </test>
>>     </tests>
>> ......................
>> 
>> 
>> Thanks,
>> G.JanakiRam
>> 
>> 
>> 
>> 
>> On Thu, Mar 27, 2014 at 3:27 PM, Janaki Rama Rao Gollapudi 
>> <janakiram.gollap...@india.semanticbits.com> wrote:
>> Hi,
>> 
>> I found below resources:
>>  Running test
>> Writing Functional tests
>> 
>> Thanks,
>> JanakiRam
>> 
>> 
>> On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama Rao Gollapudi 
>> <janakiram.gollap...@india.semanticbits.com> wrote:
>> Hi,
>> 
>> I have implemented a custom tool which will parse a given string in to 
>> expected format. Installed this custom tool into galaxy and was able to run 
>> successfully. 
>> 
>> I would like to add test cases to this tool, can you please provide me 
>> resources to write test cases for this custom tool. 
>> 
>> Is this tool need functional, unit, integration test cases ? I am not sure 
>> about which test cases needed for this tool. 
>> 
>> 
>> Thanks,
>> JanakiRam
>> 
>> 
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> 

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