Hi Gauthier, Mike, I performed the change as discussed. The user can now select one of the five options when choosing raw data files or peak lists.
Since this is a big change that affects almost all modules of MZmine, I would really appreciate if you guys could help me testing it - especially in the batch mode. You can download the beta version of MZmine 2.15 here: https://www.dropbox.com/s/zhp2nf3vq99zbj3/MZmine-2.15-beta.zip?dl=0 Please let me know if you find any problems. Tomas > On Apr 19, 2015, at 21:02, Gauthier Boaglio <gauthier.boag...@gmail.com> > wrote: > > Hi Tomas, > > It certainly would ;), but this also would mean struggling back with the > old design. As far as I remember, you changed drastically the model to > get rid of the error prone (from dev point of view) system allowing to > register the files generated by a given step. I'am not sure what is in > play here, but I suppose, since you suggest a "use files generated by > the previous step (in batch mode)" option, that you figured out a way to > keep a clean and simple global model, and have this feature restored in > the mean time (again, the piece of discussion we had at the time you > changed the model). I am not up to date with the actual current model. > Anyway, the options you are listing below would clearly make me happy > (as a user, at least)... And this is the most important (as a dev, we > always can adjust). Sounds like I want to have my cake and eat it, here, > isn't... it ;)? > > I'll checkout the current MZmine source code, and see how it looks like > ASAP, this way I'll probably be in a more comfortable position to make > pertinent comments ;). > > Cheers, > Gauthier > > > On 04/19/2015 04:54 AM, Tomas Pluskal wrote: >> 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 >> > > > -- > 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 ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
