add py requirement and actually output

[bernt-matthias]

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[bebatut]

Thanks @bernt-matthias for this update.
I just realized I already made the changes (but forgot to push. fixed now) and updated the wrapper on the ToolShed in September. Sorry for that.

I wander. Did you get an error with the new version?

[bernt-matthias]

I wander. Did you get an error with the new version?

One of my users reported an error with v 0.1.0

  File "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/31394a0c0242/combine_metaphlan2_humann2/combine_metaphlan2_humann2.py", line 87
    print "no", genus, "found in", args.metaphlan2_file
             ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("no", genus, "found in", args.metaphlan2_file)?

So in this PR only quoting the python tool directory remains.

[bernt-matthias]

Btw. shall we setup IUC style github actions on this repo?

[bernt-matthias]

The version in the toolshed seems to still miss the python2 requirement.

[bebatut]

It should be working with Python 3 now

[bebatut]

Btw. shall we setup IUC style github actions on this repo?

Maybe. But I have no idea how it works (I was in parental leave the whole year). I could maybe also move these wrappers to IUC

[bernt-matthias]

It should be working with Python 3 now

One still needs the requirement, e.g. for cases where the system has python 2. Let me just add it here.

Just understood why my user used the old version: he is using the GTN workflow which is probably using 0.1.0

Maybe. But I have no idea how it works (I was in parental leave the whole year). I could maybe also move these wrappers to IUC

The change should be pretty simple. I could create a PR, and you would need to add the TS API keys in the settings.

• For pull requests it also lints python and R scripts in addition to tool linting and testing (furthermore tests are executed using containerized testing)
• Furthermore a weekly test of all tools is executed.

But moving to IUC is also a good idea but probably more work. Up to you.

[bernt-matthias]

Finished from my side. Should I bump the tool version?