cutadapt improvements

[bernt-matthias]

fixes #5099

While working on this I have noted some more room for improvement. special attention is needed here IMO:

• the internal parameter has been dropped. while the implementation was probably not good anyway (the set value applied to all adapters which was likely not intended), the current implementation does not allow adding the X for builtin adapters.

Maybe I find the time to add some missing parameters ...

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

[bernt-matthias]

Do you want to have another look on this @mvdbeek ?

[mvdbeek]

thanks a lot @bernt-matthias!

[lldelisle]

Hi guys,
I've run this tool on my old instance (22.01) and it failed because the cut argument has moved from the section library.r1 to the section read_mod_options but the command line uses str($cut) so my instance says:

Traceback (most recent call last):
  File "/data/galaxy/galaxy/server/lib/galaxy/jobs/runners/__init__.py", line 248, in prepare_job
    job_wrapper.prepare()
  File "/data/galaxy/galaxy/server/lib/galaxy/jobs/__init__.py", line 1202, in prepare
    self.command_line, self.version_command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
  File "/data/galaxy/galaxy/server/lib/galaxy/tools/evaluation.py", line 448, in build
    global_tool_logs(self._build_command_line, config_file, "Building Command Line")
  File "/data/galaxy/galaxy/server/lib/galaxy/tools/evaluation.py", line 77, in global_tool_logs
    raise e
  File "/data/galaxy/galaxy/server/lib/galaxy/tools/evaluation.py", line 73, in global_tool_logs
    return func()
  File "/data/galaxy/galaxy/server/lib/galaxy/tools/evaluation.py", line 465, in _build_command_line
    command_line = fill_template(command, context=param_dict, python_template_version=self.tool.python_template_version)
  File "/data/galaxy/galaxy/server/lib/galaxy/util/template.py", line 107, in fill_template
    raise first_exception or e
  File "/data/galaxy/galaxy/server/lib/galaxy/util/template.py", line 80, in fill_template
    return unicodify(t, log_exception=False)
  File "/data/galaxy/galaxy/server/lib/galaxy/util/__init__.py", line 1080, in unicodify
    value = str(value)
  File "/data/galaxy/galaxy/venv/lib/python3.8/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1716409893_2057257_87444.py", line 608, in respond
NameMapper.NotFound: cannot find 'cut'

Would you mind to fix this or change the profile version?
Thanks.

[mvdbeek]

It's a bug one way or another, the parameter should be fully qualified (i.e str($read_mod_options.cut))

[mvdbeek]

Which version is that happening on @lldelisle ? This seems to be fixed in the latest version at least ?

[lldelisle]

Maybe I just ran an iwc rna-seq workflow and it was version 4.4+galaxy1