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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
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mothur: output #1472

Closed bernt-matthias closed 6 years ago

bernt-matthias commented 7 years ago

The mothur tools output the actual output and the log.

  1. The preview of the actual data set shows the content of the log.
  2. Is it possible to include the log file only if it contains any useful information? Or make it optional?

The output currently looks like this. 



mothur v.1.36.1
Last updated: 7/27/2015

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program

mothur > make.group(fasta=fasta_0.dat-fasta_1.dat,groups=pampa-anguil)

Output File Names: fasta_0.fasta_1.groups

mothur > quit
bernt-matthias commented 7 years ago

I just discovered that mothur has a -q or --quiet command line switch. As long as important messages are still printed this seems to be a good idea.

But it seems to work only with a batch file...

shiltemann commented 7 years ago

I included the log file as output because some of my users who were used to using mothur in interactive mode still really wanted to see this output for a lot of the commands, but if you feel it clutters the history too much I could add a checkbox to indicate whether you want this output or not, sure :)

bernt-matthias commented 7 years ago

Indeed log output can be important. Its a good idea to keep it if it contains useful information. Maybe for the next version of the wrappers one can incorporate the --quite parameter and add the log files only if it contains anything..?

bernt-matthias commented 7 years ago

Another idea for the next version that might help galaxy users to get informations on the tools. For the documentation calls like cluster.split(citation) could extract the original citations automatically.

shiltemann commented 7 years ago

ah, thanks for the tip :+1:

bernt-matthias commented 6 years ago

Another tip: cluster.split(help) outputs help text .

bgruening commented 6 years ago

Hopefully fixed with: https://github.com/galaxyproject/tools-iuc/pull/1722