'Galaxy local, how to display code output?
finally, I managed to load my custom tool into Galaxy. What I need is to give as input the ID of a gene and retrieve some data to be stored/displayed in a table. Now my python code is storing this table in a tab file but I’m not able to display it in Galaxy.
That’s my XML file for the tool:
<tool id="get_pheno" name="Get phenotypes" version="0.1.0">
<description>for a gene from IMPC</description>
<requirements>
<requirement type="package" version="3.8">python</requirement>
<requirement type="package" version="2.18.4">requests</requirement>
<requirement type="package" version="0.8.9">tabulate</requirement>
<requirement type="package" version='8.0.1'>IPython</requirement>
</requirements>
<command><![CDATA[python3 '${__tool_directory__}/get_pheno.py' '$input' '$output']]></command>
<inputs>
<param name="input" type='text' label='Input gene:'/>
</inputs>
<outputs>
<data format="tabular" name="output" label='${tool.name} on ${input}' />
</outputs>
<help>
This tool retrieves a list of phenotypes related to a gene entered by the user. The input must be an MGI id.
</help>
</tool>
In my code, I'm saving the list of results in a .tab file (called 'output.tab'). If I simply print the list, I don't get the table in the results but simply the values inside the "info" box in the "edit dataset attribute" tab.
I tried substituting “data” with “output” but it’s not working, I get the error 'Unable to finish the job'.
How can I get the output as a table? I already tried to read some documentation (like this guide) but I didn’t find anything useful for me. Thank you for the help
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