Perfect this is working! thanks Jochen On 04.01.2017 13:27, Devon Ryan wrote:
Try the following:
<outputs> <data format="bam" name="bam_file1" label="${tool.name} on ${on_string}: sorted.dedup.bam" from_work_dir="out.sorted.dedup.bam" /> <data format="bam" name="bam_file2" label="${tool.name} on ${on_string}: sorted.markdup.bam" from_work_dir="out.sorted.markdup.bam" /> <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log" from_work_dir="out_dup_log.txt" /> </outputs>
If you have it output to the working directory then that might solve the problem.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Wed, Jan 4, 2017 at 1:18 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Thanks Devan,
I just changed it! I have an other question. I used this to catch the output files:
<outputs> <data format="bam" name="bam_file1" label="${tool.name} on ${on_string}: sorted.dedup.bam"> <discover_datasets pattern="out.sorted.dedup.bam" format="bam" visible="true" /> <!-- can use ext or format attribute. --> </data> <data format="bam" name="bam_file2" label="${tool.name} on ${on_string}: sorted.markdup.bam"> <discover_datasets pattern="out.sorted.markdup.bam" format="bam" visible="true" /> <!-- can use ext or format attribute. --> </data> <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"> <discover_datasets pattern="out_dup_log.txt" format="txt" visible="true" /> </data> </outputs>
my problem is that I first get an empty file in the history and after some moments I also get 3 more history icons containing the actual information:
304 NuGen nudup on data 266 and data 278: sorted.markdup.bam empty 308 NuGen nudup on data 266 and data 278: sorted.markdup.bam (None) 506.3 MB
with an additional (None) in the history name? Any ideas?
Cheers Jochen
On 04.01.2017 13:10, Devon Ryan wrote:
Hi Jochen,
Don't have it use /tmp, but rather the current working directory and then everything will work. Galaxy jobs are run in individual working directories, so you can exploit that to ensure that files aren't overwritten.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Wed, Jan 4, 2017 at 12:32 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi,
I have a tool that produces multiple output files a log file, two bam files. (https://github.com/nugentechnologies/nudup)
The tool it self provides an option called --out to specify a path to a directory with a prefix that will be added to the output files:
--out /tmp/out
this will produce 3 files:
/tmp/out_dup_log.txt /tmp/out.sorted.dedup.bam /tmp/out.sorted.markdup.bam
so my question is if this out prefix will give me problems overwriting next output files coming from this tool?
Cheers Jochen
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/