Question: let other program to use my own program's outputs..
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fantasticpjyao • 0 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
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modified 4.1 years ago
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Jennifer Hillman Jackson ♦ 25k
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4.1 years ago by
fantasticpjyao • 0
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.
How did you add your program to Galaxy? Are your .ped datasets visible in some history in the UI?
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
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<?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>
Please see the following tutorial, that might help you with your tool development: https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial