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Question: Galaxy tool input and output files help please!
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gravatar for j.gao
2.4 years ago by
j.gao • 0
j.gao • 0 wrote:

Hi All,

I am a newbie to Galaxy. I created a tool in Galaxy. The tool will take 5 input parameters, 2 .txt files, 2 .csv files and 1 string as path. The tool output many files in a folder. The number of output files varies depending on the input dataset. I don't know how to configure the <outputs> tag in the .xml file to make the tool run properly. Currently, I leave <outputs> tag empty, the tool keeps the status "This job is currently running" forever. I think I need proper configuration for <outputs>. Can you provide some examples please? The wiki content gives little helpful information in this case.

Thank you very much.

Best, J
output tool input • 1.1k views
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modified 2.4 years ago by Martin Čech ♦♦ 4.9k • written 2.4 years ago by j.gao • 0

Thank you very much Katherine. I will have a look. Any further question I will be back to you.

Best,

J

ADD REPLY • link written 2.4 years ago by j.gao • 0
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gravatar for katherine.beaulieu014
2.4 years ago by
katherine.beaulieu014 • 80
katherine.beaulieu014 • 80 wrote:

Look at this forum post and try to copy the output file name for your output files. https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-August/020361.html You output tag should look like a regular output tag, like for just one file.
ADD COMMENT • link modified 2.4 years ago • written 2.4 years ago by katherine.beaulieu014 • 80

Hi Katherine,

Sorry I still have no clue what to do. My tool is a docker container built based on r. The running command is a R script with input parameters -i input dataset(txt) -o output folder(string) -p options (txt) -u template(csv) -l targeted compounds(csv). The docker runs OK directly by docker run. In the .xml file, inside <command> tag, I have given -i ${input1} -o ${input2} -p ${input3} -u ${input4} -l ${input5} . If the docker runs properly, the output files will include .txt, .csv and .pdf files. If follow the example in the post, shall I have myTool.R $input1 $input2 $input3 $input4 $input5 $output1 $output1.id $__new_file_path__ ? I am so confused. Please help me out of this. Thank you very much.

Best,

J

ADD REPLY • link modified 2.4 years ago • written 2.4 years ago by j.gao • 0
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