Question: let other program to use my own program's outputs..
0
gravatar for fantasticpjyao
3.6 years ago by
Taiwan
fantasticpjyao0 wrote:

Dear all,

I have put a program which is written in C on my Galaxy Server..

the program outputs many .ped files (depend on how many batch user enter) and a log file..

How could I let other program to use those .ped files??

:P

 

tool ped output dataset • 734 views
ADD COMMENTlink modified 3.5 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by fantasticpjyao0

I don't understand the question. Every program that can accept PED files should be able to take this as input. Just write a Galaxy tool that takes as <input> a PED file.

ADD REPLYlink written 3.6 years ago by Bjoern Gruening5.0k

How did you add your program to Galaxy? Are your .ped datasets visible in some history in the UI?

ADD REPLYlink written 3.6 years ago by Martin Čech ♦♦ 4.6k

 

I add my program in my local Galaxy Server by uploading the executable file and a xml file to "galaxy-dist/tools/myTools folder".

After execute my program, I can see the log file in history but no .ped datasets.

below is my xml file

------------------------------------------------------------------------------------------------------

<?xml version="1.0"?>

<tool id="test" name="test" version="2" tool_type="data_source">
    <command>../../../../tools/myTools/test $command</command>
    <inputs action="http://xxx.xxx.xxx.xxx/generateCommand.html" check_values="false" method="get">
        <display>go to test page $GALAXY_URL</display>
        <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
        <param name="tool_id" type="hidden" value="test" />
        <param name="sendToGalaxy" type="hidden" value="1" />
        <param name="hgta_compressType" type="hidden" value="none" />
    </inputs>
    
    <request_param_translation>
        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
        <request_param galaxy_name="URL" remote_name="URL" missing="" />
        <request_param galaxy_name="command" remote_name="command" missing="" />
    </request_param_translation>
    
    <uihints minwidth="660"/>
    <outputs>
        <data name="log_file" format="txt" from_work_dir="test/test_result.txt" label="${tool.name}"/>
    </outputs>
    <options sanitize="False" refresh="True"/>
</tool>

ADD REPLYlink written 3.6 years ago by fantasticpjyao0

Please see the following tutorial, that might help you with your tool development: https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial

ADD REPLYlink written 3.5 years ago by Martin Čech ♦♦ 4.6k
0
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Resolved? 

ADD COMMENTlink written 3.5 years ago by Jennifer Hillman Jackson25k

not yet...

:(

ADD REPLYlink written 3.5 years ago by fantasticpjyao0

See Martin's reply above. Create an output dataset (or datasets, as needed) in the history. When the tool is used, intermediate datasets can be managed to reduce history clutter. In the history itself or in a workflow.

Hope this helps! Jen, Galaxy team

ADD REPLYlink written 3.5 years ago by Jennifer Hillman Jackson25k
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