Hi, I have workflows where I would like to rename the item at each step. The reason for this to have a proper naming. What I did is to use the renaming option in the workflow editor. I specified the 'New output name:' to ${input} This does not work. Is there any variable which works or is there a easy way in doing this? Any help or hint is appreciated. Cheers Manuel -- Manuel Kohler Center for Information Sciences and Databases (C-ISD) Department of Biosystems Science & Engineering (D-BSSE) ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132
The renaming input selector uses # instead of $ to allow combinations with workflow parameters. So, in your case, #{input} should work. There are also options (basename, upper, lower) that you can use to format the text. So, #{input | upper} would use the input name but ensure that it was all uppercase. -Dannon On Sep 26, 2012, at 8:23 AM, Kohler Manuel <manuel.kohler@bsse.ethz.ch> wrote:
Hi, I have workflows where I would like to rename the item at each step. The reason for this to have a proper naming. What I did is to use the renaming option in the workflow editor. I specified the 'New output name:' to ${input} This does not work. Is there any variable which works or is there a easy way in doing this? Any help or hint is appreciated.
Cheers Manuel
-- Manuel Kohler Center for Information Sciences and Databases (C-ISD) Department of Biosystems Science & Engineering (D-BSSE) ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Dannon, thanks for the fast reply. I changed it to #{input}. But all the data names are still empty. Is there anything I am missing? BTW: I am on r7720 Cheers Manuel On 26. September 2012 4:10 PM, "Dannon Baker" <dannonbaker@me.com> wrote:
The renaming input selector uses # instead of $ to allow combinations with workflow parameters.
So, in your case, #{input} should work. There are also options (basename, upper, lower) that you can use to format the text. So, #{input | upper} would use the input name but ensure that it was all uppercase.
-Dannon
On Sep 26, 2012, at 8:23 AM, Kohler Manuel <manuel.kohler@bsse.ethz.ch> wrote:
Hi, I have workflows where I would like to rename the item at each step. The reason for this to have a proper naming. What I did is to use the renaming option in the workflow editor. I specified the 'New output name:' to ${input} This does not work. Is there any variable which works or is there a easy way in doing this? Any help or hint is appreciated.
Cheers Manuel
-- Manuel Kohler Center for Information Sciences and Databases (C-ISD) Department of Biosystems Science & Engineering (D-BSSE) ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Ahh, I see what's probably going on. The matching uses the tool's actual input name (which isn't exposed, and isn't always 'input') as opposed to the label that you'll see in the tool form and elsewhere. Which tool is this for? If you look at the tool xml file you should see the real input name and can try that. On Sep 26, 2012, at 10:32 AM, Kohler Manuel <manuel.kohler@bsse.ethz.ch> wrote:
Hi Dannon, thanks for the fast reply. I changed it to #{input}. But all the data names are still empty. Is there anything I am missing?
BTW: I am on r7720
Cheers Manuel
On 26. September 2012 4:10 PM, "Dannon Baker" <dannonbaker@me.com> wrote:
The renaming input selector uses # instead of $ to allow combinations with workflow parameters.
So, in your case, #{input} should work. There are also options (basename, upper, lower) that you can use to format the text. So, #{input | upper} would use the input name but ensure that it was all uppercase.
-Dannon
On Sep 26, 2012, at 8:23 AM, Kohler Manuel <manuel.kohler@bsse.ethz.ch> wrote:
Hi, I have workflows where I would like to rename the item at each step. The reason for this to have a proper naming. What I did is to use the renaming option in the workflow editor. I specified the 'New output name:' to ${input} This does not work. Is there any variable which works or is there a easy way in doing this? Any help or hint is appreciated.
Cheers Manuel
-- Manuel Kohler Center for Information Sciences and Databases (C-ISD) Department of Biosystems Science & Engineering (D-BSSE) ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
<Screen shot 2012-09-26 at 4.31.34 PM.png>
Hi, now it works :-) To be honest, this should be in the documentation for sure. Some people complain that the naming is just a mess. Here a normal use case why: I processed 15 files downloaded from GEO with this workflow: 1. load FASTQ 2. align with Bowtie 3. convert to BAM 4. convert to bigWig When you look at the bigWig files in UCSC the naming is completely lost and you do not know which file is which. So you need to dig all the data tree back to the initial FASTQ file. So just for completeness the variables which are currently valid are: tool_id=bowtie_wrapper: #{sInput1} tool_id=sam_to_bam: #{input1} tool_id=bam_to_bigwig: #{align} This leads to the nice naming in the screen shot. Cheer Manuel On 26. September 2012 4:38 PM, "Dannon Baker" <dannonbaker@me.com> wrote:
Ahh, I see what's probably going on. The matching uses the tool's actual input name (which isn't exposed, and isn't always 'input') as opposed to the label that you'll see in the tool form and elsewhere. Which tool is this for? If you look at the tool xml file you should see the real input name and can try that.
On Sep 26, 2012, at 10:32 AM, Kohler Manuel <manuel.kohler@bsse.ethz.ch> wrote:
Hi Dannon, thanks for the fast reply. I changed it to #{input}. But all the data names are still empty. Is there anything I am missing?
BTW: I am on r7720
Cheers Manuel
On 26. September 2012 4:10 PM, "Dannon Baker" <dannonbaker@me.com> wrote:
The renaming input selector uses # instead of $ to allow combinations with workflow parameters.
So, in your case, #{input} should work. There are also options (basename, upper, lower) that you can use to format the text. So, #{input | upper} would use the input name but ensure that it was all uppercase.
-Dannon
On Sep 26, 2012, at 8:23 AM, Kohler Manuel <manuel.kohler@bsse.ethz.ch> wrote:
Hi, I have workflows where I would like to rename the item at each step. The reason for this to have a proper naming. What I did is to use the renaming option in the workflow editor. I specified the 'New output name:' to ${input} This does not work. Is there any variable which works or is there a easy way in doing this? Any help or hint is appreciated.
Cheers Manuel
-- Manuel Kohler Center for Information Sciences and Databases (C-ISD) Department of Biosystems Science & Engineering (D-BSSE) ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
<Screen shot 2012-09-26 at 4.31.34 PM.png>
participants (2)
-
Dannon Baker -
Kohler Manuel