make tools compatible with IUC guidelines

[bgruening]

The IUC has some guidelines developed to make tools secure and improve UX across different tools.

You can learn more here: https://galaxy-iuc-standards.readthedocs.io

Important security fixes:

• use single quotes for all data parameters, text parameters and all things that contain a path. E.g. $__tool_directory__. e.g. https://github.com/TAMU-CPT/CPT-ToolshedSource/blob/main/cpt_blastp_to_gff/blastp_to_gff3.xml#L9 but also $outputs https://github.com/TAMU-CPT/CPT-ToolshedSource/blob/main/cpt_blastp_to_gff/blastp_to_gff3.xml#L17 or https://github.com/TAMU-CPT/CPT-ToolshedSource/blob/main/cpt_fasta_remove_id/fasta_remove_id.xml#L10

small things

• it would be nice to add a tool-profile https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-profile to each tool
• interpreter="python" should not be used anymore, instead use python script in your command line.
• size="5" and similar can be removed from parameters
• please use 4 spaces intend and no spaces

If you like also look at https://github.com/galaxyproject/galaxy-language-server which will lint your tools and help spot some stuff.

[bgruening]

@jasonjgill do you think anyone in your team can work on this? Happy to review any PR in this direction.

[jasonjgill]

@bgruening I responded in the galaxy PR, but we can make these changes if this is needed for hosting on Galaxy. @cross12tamu is our coder/developer, I can work with him to see how much time these changes will take. Are these changes so the tools can be taken up into IUC?

[bgruening]

Those are the IUC recommendations, yes. But the quoting issues I raised are actually security concerns. So independently of IUC those should be fixed before we deploy them on EU. Sorry :(

[cross12tamu]

I'll take a look at this!