Merging changes from Martin's (althonos) repo to Tom's (tomnl) #2
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…ools. Registered a system command 'mzml2isa' to call from terminal. Factored xpaths to be called independently from versions. Removed build folder from repo as it is generated automaticaly by setup.py
… highlights for code in README.md. Made it so the parser now sorts files alphabeticaly (so that ouput is consistent and easier to read.
…sts on other mzML files (from HUPO-PSI/mzML repo). Added a to-do list.
…ss to attributes. Made two separate cases for instruments parsing. Added a build_env method that looks for specific vocabulary of parsed file. Added metabolights.py script that downloads studies from MetaboLight and build isa files out of i
…sa on every study of MetaboLights (EBI) containing .mzML
…/mbtls_builds.txt for tests results)
…are now processed into an url to the obolibrary url concerning said number.
…ght term in isa study file). United most variables of ISA_Tab into a dict for easy access with formating. Changed the way default ISA files are read so now that only the two first lines are needed (without that it led to a bug where only the nth first studies were written in the ISA study file, n being the number of lines of the default study file...
…t overwritten and just ignored
…ion. Corrected crash occuring when no instruments were found in mzML file.
…lity. Started building a system for investigation and study files templating with user-generated informations. Edited **scripts/metabolights-dl.py** so that it now parses the files it downloads. Corrected a case of obo file staying unclosed after parsing.
…mns from assay template.
…e section to mzml module. Removed m/z range warning for imzML.
Add bioconda badge
Issue referenced here: https://github.com/althonos/mzml2isa-qt/issues/6 Fix taken here: http://stackoverflow.com/a/3348664 thanks @proccaserra for having found the bug !
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Psssst @Tomnl, could you add me as a contributor now that you're omnipotent ? 😄 |
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Alas, I am no longer omnipotent. My admin rights were only temporary. Please could someone from ISA-tools (@djcomlab @proccaserra, @agbeltran) add the mzml2isa repo to the mzml2isa-galaxy team and then change the team name to 'xml2isa'. I think we will be sorted after that. |
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I have added the mzml2isa repository to the team and changed the name. |
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Great ! Thanks Alejandra ! |
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Thanks 👍 |
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May I also have write access to ISA-Tools/mzml2isa ? Or do you want me to continue developing on my fork, submitting occassional patches through pull requests ? |
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Sorry I forgot to ask for admin access. @agbeltran : Sorry to be a pain but could you change the settings for the repo xml2isa to be admin. e.g. like the mzml2isa-galaxy and nmrml2isa-galaxy |
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Done. And I see that @althonos is already in the team. |
My mzml2isa repo is now quite far out of date but is still referenced in search engines. To avoid confusion I am updating the repo with the most recent changes from Martin.
I will then transfer ownership to ISA-Tools. The development of the tool will then continue at ISA-Tools/mzml2isa. See issue 1.