Bioinformatics with Python Cookbook - Second Edition

How to do it…

Take a look at the following steps:

1. We start by asking planemo to create a scaffold configuration for our tool:

planemo tool_init --id bioinf_test --name "Basic BED analyzer"

This will generate a file called bioinf_text.xml. Please inspect it, as most of the next steps will require changing it.

2. Start by linting the file:

planemo lint  # You can also do only planemo l

This is the Planemo linting tool, and you will see that there are some problems with the file.

3. Let's add some help text. Replace the <help>...</help> section with:

<help><![CDATA[   A Basic BED analyzer.   Counts entries and optionally reports basic stats]]></help>

Lint again, just to make sure no more errors were introduced. It still fails, but no new error should ...