Hi all, For these parameters, 'input' refers to the exact tool input name. Recent versions of Galaxy will now tell you what the options are to use, like the following I see for bowtie2: [image: Inline image 1] I definitely agree that it's not intuitive, and I'm trying to think of ways to make this better -- suggestions definitely welcome. -Dannon On Wed, Nov 12, 2014 at 6:54 AM, Langhorst, Brad <Langhorst@neb.com> wrote:
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 <https://bitbucket.org/galaxy/galaxy-central/commits/d1e1beeb532239250396dd8fbdc0156508c6744e>
Can anyone help me, please? Jan
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