Rename output file on workflow

[methylome]

I've tried to use this function for the output of tophat V0.7 for the input of a list of paired files, i.e, list:paired. First, #{input} doesn't work although it's a parameter name as shown below.
<when value="paired_collection"> <param format="fastqsanger" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ paired reads" help="Must have Sanger-scaled quality values with ASCII offset 33" /> <expand macro="paired_parameters" /> </when>
Second, #{input1}, which means the first file name, works but all paired datasets have the same output name. For instance, given a list of two paired files: hgrna1 and hgrna2, each of which has two fastq files, two output bam file names are the same as hgrna1_R1.bam.

Is this a known bug?

Thanks,
Justin.

[jmchilton]

Is this the same problem as #1675?

• We need a more descriptive UI to show both element identifier and name for collection items.
• And we need PostJobActions for mapped over output collections. #1680 - to be able to rename collection names on mapped steps of a workflow.

[dannon]

@jmchilton yes, I think so. Per conversation in IRC yesterday I started taking a look here at the various issues with the rename action and am hoping to get a fix out today.

[chambm]

@dannon Is this supposed to be fixed? I have this problem with HISAT. See this simple test workflow at:
http://129.114.18.155/u/chambm/w/hisat-rename-test

This is a fresh 17.01 Galaxy hosted on Jetstream.

[dannon]

@chambm Let me doublecheck, but yeah, I thought this was resolved.

('close and comment' button fail, sorry)

[chambm]

Did you have a chance to check?