Question: What is the difference between a label and name?
gravatar for m93
7 days ago by
m930 wrote:

I am very new to Galaxy and am learning about workflows with the final aim of making a workflow for RNAseq differential expression analysis.

I was wondering if someone could clarify for me the difference between a "Label" and "Dataset name".

  • Is the Label the name you see for an individual dataset or collection in your history panel?
  • Is the dataset name the actual "real name" that the file has?

An example might be clearer:

I have a history that looks like this:

 99: FastQC on collection 79: Raw Data
 a list of 18 items

 98: FastQC on collection 79: Webpage
 a list of 18 items

 79: Trim Galore! on collection 40: trimmed reads
 a list of 18 items

 42: FastQC on collection 40: RawData
 a list of 18 items

 41: FastQC on collection 40: Webpage
 a list of 18 items

 40: raw-fastq.gz
 a list of 18 items

The first item of this history, 40, was made by importing 18 fastq.gz files: sample1.fastq.gz, sample2.fastq.gz, sample3.fastq.gz etc and putting them into a simple (unpaired) collection called "raw-fastq.gz."

  • Now, when I click on "40: raw-fastq.gz", it shows all 18 fastq.gz files named as they were when they were imported: sample1.fastq.gz, sample2.fastq.gz etc. If I click on info (i symbol) for a given fastq.gz file, it will show "Name: sample1.fastq.gz". So far so good, all seems normal.

  • But when I click on 41: FastQC on collection 40: Webpage, it shows 18 files ALSO named sample1.fastq.gz.. But these files are not fastq.gz files, they are html reports! And when I click on a file, for example, sample1.fastq.gz, this time the info page will show "Name: FastQC on data 22: Webpage".

So I'm confused: are the names that appear on the history panel "Labels" and the real names of files (i.e. the ones used on the Galaxy server, let's say) found in the "Name:" entry of the info page? I find this distinction very confusing, especially when trying to build workflows in which you can change labels and names of outputs..

  • When only working with simple datasets, it seems that Label = Name
  • When working with collections, the Label is not always equal to the Name?

Many thanks

label name galaxy • 31 views
ADD COMMENTlink modified 1 day ago by Jennifer Hillman Jackson25k • written 7 days ago by m930
gravatar for Jennifer Hillman Jackson
1 day ago by
United States
Jennifer Hillman Jackson25k wrote:


The dataset name displayed in the GUI is not the actual file name of the dataset on disk. Click into the Job Details page ("I" icon) per dataset to view the path to the file on disk if curious.

Tools do not use the displayed dataset names to determine if an input is of the correct format/type. Datatype, database, and other metadata are used instead. This is why it is fine to change an output's name when customizing a workflow - Galaxy has an internal path/name for the data. The internal names are not important to consider when constructing a workflow (dataset file names are encoded and have nothing to do with the displayed name).

More about Dataset Collections is here:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 1 day ago by Jennifer Hillman Jackson25k
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