Hi Gauthier, Mike, I can imagine the file selector could have several options:
* use all files * use currently selected files (in the GUI) * use files generated by the previous step (in batch mode) * select files manually * select files using name pattern Would that make you happy? :) Cheers, Tomas > On Apr 19, 2015, at 1:48 AM, Gauthier Boaglio <gauthier.boag...@gmail.com> > wrote: > > Hi all, > > Sounds like something that went on the table earlier ;) > > https://sourceforge.net/p/mzmine/mailman/message/33158142/ > > The old way / design (before 2.13) was handy from user point of view > because each step was getting automatically the files generated by the > previous step as input for the next step, but was also causing issues > (more from link above). > > Well, don't know if a compromise could be found. As a matter of fact, > setting wildcards filtering for each step is constraining, from user side... > > Best, > Gauthier > > > On 04/18/2015 04:31 AM, Tomas Pluskal wrote: >> Hi Mike, >> >> In the selection component you can use wildcards (*) to specify the names of >> raw data files that will be used. >> >> For example >> * will use all files >> *filtered will use all files with name ending with "filtered" >> >> And so on. This way you can "program" the batch mode to use exactly the >> right files in each step. >> >> Thinking about that, we could probably add an extra option "Use the files >> currently selected in the project window". That would be useful for the >> first step of the batch. I'll take a look at it later. >> >> Best, >> >> Tomas >> >> >> >>> On Apr 18, 2015, at 1:28 AM, Williams,Michael Thomas David >>> <mtdwilli...@ufl.edu> wrote: >>> >>> Hello, >>> >>> I am having trouble running batch mode analysis using v. 2.14.2 (newest). >>> In older versions (2.12 specifically) we are able to select all of the >>> imported files and run a batch mod on all files without selecting specific >>> file names for each process in the batch. >>> >>> Is there a way to do something similar with the current version? As it is >>> now I have to manually select the files for each step in the batch >>> sequence. Which at first is only the raw files. It runs through the Mass >>> detection, but because old lists are replaced by new ones (with new names) >>> in each subsequent step we get an error and these then have to be run >>> manually since the peak list names change with each step (chromatogram >>> builder, deconvolution, isotopic grouper, join aligner, etc.). Can this be >>> fixed so that the batch process will work? This tends to save us a lot of >>> time without having to come back to run each process manually. >>> >>> Thanks, >>> Mike >>> >>> >>> Michael D. Williams >>> Postdoctoral Research Associate >>> University of Florida >>> mtdwilli...@ufl.edu >>> ------------------------------------------------------------------------------ >>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT >>> Develop your own process in accordance with the BPMN 2 standard >>> Learn Process modeling best practices with Bonita BPM through live exercises >>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ >>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF_______________________________________________ >>> Mzmine-devel mailing list >>> Mzmine-devel@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel >> =============================================== >> Tomas Pluskal >> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University >> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan >> WWW: https://groups.oist.jp/g0 >> TEL: +81-98-966-8684 >> Fax: +81-98-966-2890 >> >> >> ------------------------------------------------------------------------------ >> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT >> Develop your own process in accordance with the BPMN 2 standard >> Learn Process modeling best practices with Bonita BPM through live exercises >> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ >> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF >> _______________________________________________ >> Mzmine-devel mailing list >> Mzmine-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/mzmine-devel > > > -- > Gauthier BOAGLIO > CEFE - UMR 5175 > 1919 route de Mende > F-34293 Montpellier cedex 5 > > Tel: +33/0 4 67 61 32 15 > Fax: +33/0 4 67 61 33 36 > > email: gauthier.boag...@cefe.cnrs.fr > www: > http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio > http://www.evolepid.org/people.php?name=boaglio > > > ------------------------------------------------------------------------------ > BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT > Develop your own process in accordance with the BPMN 2 standard > Learn Process modeling best practices with Bonita BPM through live exercises > http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ > source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF > _______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan WWW: https://groups.oist.jp/g0 TEL: +81-98-966-8684 Fax: +81-98-966-2890 ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
