Some Galaxy Tools Merge results into a single file and we need an indicator of this in the UI

[scottx611x]

• Specific code commit: 7e8847f
• Version of the web browser and OS: any
• Environment where the error occurred (Vagrant VM and site conf mode or AWS instance):
  test.stemcellcommons.org

UPDATE: Read this

Steps to reproduce

1. Run an RNA-Seq (Se)/(PE) or Chip-Seq Analysis with more than one input file or input pair

Observed behavior

• Analyses will run successfully, but a subset of the derived results are imported back into Refinery
• From an RNA-Seq (SE) run with two input files. There should be 6 derived datafiles but there are only 4:
  

Expected behavior

• For the proper amount of derived datafiles to be imported back into refinery

General Notes:

• This is probably related to Analysis results are not added to source data set #2294
• All current Workflows behave appropriately when a single input file or input pair is selected
• The FastQC Workflow behaves appropriately regardless of the number of input files selected

To Do:

• Make sure that the proposed solution doesn't affect provvis rendering w/ subanlayses

[scottx611x]

Looking into this issue deeper it seems that some tools, when given a dataset collection, will just provide a single output file with merged results from the N inputs. For example: featureCounts does this.

The proposed fix at the moment is to provide logic in _get_analysis_group_number so that said number, when displayed in the ui, would be updated to reflect which inputs have been used in the merged result.

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Ex:

Run RNA Seq (SE) w/ 2 inputs:

Output Name	Analysis Group Number
accepted_hits	0
accepted_hits	1
output	0 + 1
output summary	0 + 1

[scottx611x]

Another thought here is that these files will not be merged if we name the outputs appropriately (output summary for: input1.bam, output summary for: input2.bam) etc.