Source: i2masschroq
Section: science
Priority: optional
Maintainer: The Debichem Group <debichem-devel@alioth-lists.debian.net>
Uploaders: Filippo Rusconi <lopippo@debian.org>
Build-Depends: debhelper-compat (= 12),
 dpkg-dev (>= 1.18.25),
 cmake (>= 3.12),
 qt6-base-dev,
 libpappsomspp-core-dev (>= 0.11.19),
 libpappsomspp-gui-dev (>= 0.11.19),
 libodsstream-dev (>= 0.9.19),
 libboost-dev,
 libboost-thread-dev,
 libboost-chrono-dev,
 libboost-container-dev,
 libboost-random-dev,
 libboost-filesystem-dev,
 libboost-iostreams-dev,
 libzstd-dev,
 liblzf-dev,
 libsqlite3-dev,
 qt6-svg-dev,
 qt6-svg-plugins,
 libqcustomplot-dev (>= 2.1.0),
 cutelee6-qt6-dev,
 docbook-to-man,
 libjs-jquery,
 libjs-highlight.js,
 daps,
 fonts-ebgaramond,
 fonts-ebgaramond-extra,
 doxygen,
 catch2,
 graphviz
Standards-Version: 4.6.0
Homepage: http://pappso.inra.fr/bioinfo
Vcs-Browser: https://salsa.debian.org/debichem-team/i2masschroq
Vcs-Git: https://salsa.debian.org/debichem-team/i2masschroq.git

Package: xtpcpp
Section: oldlibs
Architecture: any
Multi-Arch: no
Depends: i2masschroq,
 debconf,
 po-debconf,
 ${shlibs:Depends},
 ${misc:Depends}
Description: Transitional package from xtpcpp to i2masschroq
 The program allows one to perform the following tasks:
  -Reads X!Tandem xml results files
  -Reads MASCOT dat results files
  -Reads TPP pepXML results files
  -Reads PSI mzIdentML results files
  -Run X!Tandem analyzes through a graphical user interface
  -Implements various filters based on statistical values
  -Powerful original grouping algorithm to filter redundancy
  -Phosphopeptide mode to handle phosphoproteomics datasets
  -Edit, search and sort the data graphically
  -XIC chromatogram browser (eXtracted Ion Current)
  -Comparisons of theoretical isotope patterns to measured MS1 XIC areas
  -Export data directly to Microsoft Office 2010 and LibreOffice (ods export)
  -Handle huge datasets very quickly
  -Perform peptide quantification through MassChroQml export
 .
 This package is a transitional package. You can remove it at any time.

Package: xtpcpp-doc
Section: oldlibs
Architecture: all
Multi-Arch: no
Depends: i2masschroq-doc,
 debconf,
 po-debconf,
 ${misc:Depends}
Description: Transitional package from xtpcpp-doc to i2masschroq-doc
 The program allows one to perform the following tasks:
  -Reads X!Tandem xml results files
  -Reads MASCOT dat results files
  -Reads TPP pepXML results files
  -Reads PSI mzIdentML results files
  -Run X!Tandem analyzes through a graphical user interface
  -Implements various filters based on statistical values
  -Powerful original grouping algorithm to filter redundancy
  -Phosphopeptide mode to handle phosphoproteomics datasets
  -Edit, search and sort the data graphically
  -XIC chromatogram browser (eXtracted Ion Current)
  -Comparisons of theoretical isotope patterns to measured MS1 XIC areas
  -Export data directly to Microsoft Office 2010 and LibreOffice (ods export)
  -Handle huge datasets very quickly
  -Perform peptide quantification through MassChroQml export
 .
 This package is a transitional package. You can remove it at any time.

Package: xtpcpp-tools
Section: oldlibs
Architecture: any
Multi-Arch: no
Depends: i2masschroq-tools,
 debconf,
 po-debconf,
 ${shlibs:Depends},
 ${misc:Depends},
Description: Transitional package from xtpcpp-tools to i2masschroq-tools
 The program allows one to perform the following tasks:
  -Reads X!Tandem xml results files
  -Reads MASCOT dat results files
  -Reads TPP pepXML results files
  -Reads PSI mzIdentML results files
  -Run X!Tandem analyzes through a graphical user interface
  -Implements various filters based on statistical values
  -Powerful original grouping algorithm to filter redundancy
  -Phosphopeptide mode to handle phosphoproteomics datasets
  -Edit, search and sort the data graphically
  -XIC chromatogram browser (eXtracted Ion Current)
  -Comparisons of theoretical isotope patterns to measured MS1 XIC areas
  -Export data directly to Microsoft Office 2010 and LibreOffice (ods export)
  -Handle huge datasets very quickly
  -Perform peptide quantification through MassChroQml export
 .
 This package is a transitional package. You can remove it at any time.

Package: i2masschroq
Architecture: any
Multi-Arch: no
Depends: tandemng,
 libodsstream0 (>= 0.9.2),
 qt6-svg-plugins,
 ${shlibs:Depends},
 ${misc:Depends}
Recommends: i2masschroq-tools,
 tandemng
Provides: xtpcpp (= 0.4.54)
Replaces: xtpcpp (<< 0.4.54)
Breaks: xtpcpp (<< 0.4.54)
Description: Successor of X!TandemPipeline
 The program allows one to perform the following tasks:
  -Reads X!Tandem xml results files
  -Reads MASCOT dat results files
  -Reads TPP pepXML results files
  -Reads PSI mzIdentML results files
  -Run X!Tandem analyzes through a graphical user interface
  -Implements various filters based on statistical values
  -Powerful original grouping algorithm to filter redundancy
  -Phosphopeptide mode to handle phosphoproteomics datasets
  -Edit, search and sort the data graphically
  -XIC chromatogram browser (eXtracted Ion Current)
  -Comparisons of theoretical isotope patterns to measured MS1 XIC areas
  -Export data directly to Microsoft Office 2010 and LibreOffice (ods export)
  -Handle huge datasets very quickly
  -Perform peptide quantification through MassChroQml export

Package: i2masschroq-doc
Section: doc
Architecture: all
Depends: libjs-jquery,
         libjs-highlight.js,
         ${misc:Depends}
Provides: xtpcpp-doc (= 0.4.54)
Replaces: xtpcpp-doc (<< 0.4.54)
Breaks: xtpcpp-doc (<< 0.4.54)
Description: Successor of X!TandemPipeline (user manual)
 The program allows one to perform the following tasks:
  -Reads X!Tandem xml results files
  -Reads MASCOT dat results files
  -Reads TPP pepXML results files
  -Reads PSI mzIdentML results files
  -Run X!Tandem analyzes through a graphical user interface
  -Implements various filters based on statistical values
  -Powerful original grouping algorithm to filter redundancy
  -Phosphopeptide mode to handle phosphoproteomics datasets
  -Edit, search and sort the data graphically
  -XIC chromatogram browser (eXtracted Ion Current)
  -Comparisons of theoretical isotope patterns to measured MS1 XIC areas
  -Export data directly to Microsoft Office 2010 and LibreOffice (ods export)
  -Handle huge datasets very quickly
  -Perform peptide quantification through MassChroQml export
 .
 This package ships the user manual in both PDF and HTML formats.

Package: i2masschroq-tools
Architecture: any
Multi-Arch: no
Depends: tandemng,
 ${shlibs:Depends},
 ${misc:Depends}
Provides: xtpcpp-tools (= 0.4.54)
Replaces: xtpcpp-tools (<< 0.4.54),
  xtpcpp-tandemwrapper-dbgsym (<< 0.4.54),
  xtpcpp-tandemwrapper (<< 0.4.54)
Breaks: xtpcpp-tools (<< 0.4.54),
  xtpcpp-tandemwrapper-dbgsym (<< 0.4.54),
  xtpcpp-tandemwrapper (<< 0.4.54)
Description: X!Tandem-related utilities for timsTOF pro and modern mzML data
 The programs allow one to perform the following tasks:
 .
  - Convert and store a (partial) copy of the initial mass spectrometry
    data files in the mzXML format that is required by X!Tandem;
  - Perform the conversion above and run i2masschroq on the obtained
    data files seamlessly.
 .
 This package ships two command line tools that are useful when
 mass data are available in a format that is not immediately consumable by
 X!Tandem (like mzML or Bruker timsTOF data).
