Custom tool output displaying

, ,
6

How do you know that the tool even works? Here we established that you already have version conflicts:Galaxy local python Module Not Found Error
And because the tool will be executed in the background in a conda environment you need to execute python instead of python3.

Try to make a simple working “test” tool first. Your XML could be something like:

<tool id="my_first_test" name="test tool">
  <requirements>
    <requirement type="package" version="3.8">python</requirement>
  </requirements>

  <command>
<![CDATA[
 python '${__tool_directory__}/test.py' -i $input -o $output
]]>
</command>
  <inputs>
	  <param name="input" type="text" label="Test input" />
  </inputs>	  
  <outputs>
    <data format="tabular" name="output" label="test output" />
  </outputs>

  <help>
  </help>
</tool>

And the python code (of top of my head):

import argparse
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter, description='')
parser.add_argument('-i', dest='input', type=str, help='', required=True)
parser.add_argument('-o', dest='output', type=str, help='', required=True)
args = parser.parse_args()

with open(args.output, "a") as out:
    out.write(args.input)

And let’s go from there

Is there any way to better understand where is the error?

Is the ouput at this moment green or red?