Updating workflows/transcriptomics/rnaseq-sr from 0.4 to 0.5

[planemo-autoupdate]

Hello! This is an automated update of the following workflow: workflows/transcriptomics/rnaseq-sr. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

• toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy2

The workflow release number has been updated from 0.4 to 0.5.

[lldelisle]

Hi,
I have 2 issues with this PR:

• In the CI, I get the following error:

Unexpected HTTP status code: 400: {"err_msg": "Workflow was not invoked; the following required tools are not installed: pick_value (version 0.1.0)", "err_code": 0, "traceback": "Traceback (most recent call last):\n  File \"/tmp/tmpte_429am/galaxy-dev/lib/galaxy/web/framework/decorators.py\", line 337, in decorator\n    rval = func(self, trans, *args, **kwargs)\n  File \"/tmp/tmpte_429am/galaxy-dev/lib/galaxy/webapps/galaxy/api/workflows.py\", line 751, in invoke\n    raise exceptions.MessageException(missing_tools_message)\ngalaxy.exceptions.MessageException: Workflow was not invoked; the following required tools are not installed: pick_value (version 0.1.0)\n"}

• When I try the workflow on usegalaxy.org I have an issue: there are 2 subworkflows and only one of them should be run because they both have conditional and one is the contrary of the other. However, they both run... Any idea, why?
  Here is a 'simplified workflow':
  

[mvdbeek]

• In the CI

that'll be fixed by galaxyproject/planemo#1385

Any idea, why?

No idea, I'll see what's up with that

[lldelisle]

I can share the minimum workflow with you if you want.

[mvdbeek]

Ah yes, that would be helpful!

[lldelisle]

It seems that there is still a bug. Let see that on Monday.

[mvdbeek]

Ah, yes, a conditional workflow output, we missed that case!

[lldelisle]

It finally passes 🎉 (I put all conditional steps to true)

[mvdbeek]

Looks good, but can you apply the same language edits from the PE PR ?

[mvdbeek]

Suggested change

	- Use STAR to compute normalized strand splitted coverage
	- Use STAR to compute normalized strand-specific coverage

[mvdbeek]

Suggested change

	- Propose StringTie to compute FPKM etc...
	- Add option to use StringTie to compute FPKM

[mvdbeek]

Suggested change

	- Put cufflinks step optional
	- Make cufflinks step optional

[lldelisle]

Thanks. I combined both in #211 (was easier for me to introduce spelling changes in both places)