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: dpr...@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.b...@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: dpr...@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.b...@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
>
>
>
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