Hi Jan:

Are you using input dataset tool? I'm not sure it's required - but I habitually use it.

I'm attaching an image of a working renaming setup. I hope it helps.

brad

---

From: Jan Hapala <jan@hapala.cz>
Sent: Wednesday, November 12, 2014 9:29 AM
To: Langhorst, Brad
Subject: Re: [galaxy-dev] rename output dataset in workflow - input dataset variable

 

Thanks, Brad. This is informative, but I'm still stuck.

I have an input dataset which passes data to FASTQ Summary Statistics. (I have tried other tools, as well.)

The output file name is: stats on: #{input1}

The name of the Input dataset is: input1

I get this result: stats on:

Jan

2014-11-12 14:06 GMT+01:00 Langhorst, Brad <Langhorst@neb.com>:

For what it's worth (not much ;), I think the dataset naming is the single least intuitive part of the galaxy system for biologists.

I think there's a proposal to "fix" this problem - and mainain the connection between input data set and derived data, but It doesn't seem to have gone anywhere yet. 

Anyway, you have to check the name of the field for each tool - it's sometimes "input" and sometimes something else.

You want to use the #{} for naming.  The ${} stuff is for parameters

I also do this kind of thing: to keep the names from getting too long.

#{input_1 | basename}.bam

The basename removes everything after the last . character.

Brad

 

---

From: galaxy-dev-bounces@lists.bx.psu.edu <galaxy-dev-bounces@lists.bx.psu.edu> on behalf of Jan Hapala <jan@hapala.cz>
Sent: Wednesday, November 12, 2014 7:49 AM
To: galaxy-dev
Subject: [galaxy-dev] rename output dataset in workflow - input dataset variable

 

Hello,

I want to rename ouput datasets in a workflow in such a way that the name contains the name of the input dataset. I could not find instructions in the manual (and this info is missing in the Workflow editor - would be really helpful there!).

I tried #{input}, e.g. "stats on: #{input}" (with no quotes), but I keep getting just "stats on:" The variable is empty. When I use ${input}, I get a variable field in the workflow form (I do not want this).

My G. instance: Galaxy changeset: d1e1beeb532239250396dd8fbdc0156508c6744e

Can anyone help me, please?

Jan

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