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
