diff --git a/pythonProject/main.py b/pythonProject/main.py
new file mode 100644
index 000000000..5596b4478
--- /dev/null
+++ b/pythonProject/main.py
@@ -0,0 +1,16 @@
+# This is a sample Python script.
+
+# Press Shift+F10 to execute it or replace it with your code.
+# Press Double Shift to search everywhere for classes, files, tool windows, actions, and settings.
+
+
+def print_hi(name):
+ # Use a breakpoint in the code line below to debug your script.
+ print(f'Hi, {name}') # Press Ctrl+F8 to toggle the breakpoint.
+
+
+# Press the green button in the gutter to run the script.
+if __name__ == '__main__':
+ print_hi('PyCharm')
+
+# See PyCharm help at https://www.jetbrains.com/help/pycharm/
diff --git a/tools/i2nca/.shed.yml b/tools/i2nca/.shed.yml
new file mode 100644
index 000000000..c1cf69bec
--- /dev/null
+++ b/tools/i2nca/.shed.yml
@@ -0,0 +1,10 @@
+name: i2nca
+owner: galaxyp
+categories:
+ - Proteomics
+ - Imaging
+description: i2nca is a preprocessing software for MSI data in imzML format.
+long_description: |
+ i2nca (msI INteractive Conversion and quality Assesment) is designed to utilize the imzml parsing capabilities of m2aia and provides internal file conversions within this file type.
+ It can also perform multi-file operations and generate quality reports on imzML files.
+homepage_url: https://github.com/cKNUSPeR/i2nca
diff --git a/tools/i2nca/i2nca_agnostic_qc.xml b/tools/i2nca/i2nca_agnostic_qc.xml
new file mode 100644
index 000000000..dbccdd348
--- /dev/null
+++ b/tools/i2nca/i2nca_agnostic_qc.xml
@@ -0,0 +1,99 @@
+
+
+
+ Create agnostic quality control reports for any kind of .imzML file.
+ Different metrics will be visualized as a pdf report.
+
+
+
+ macros.xml
+
+
+
+ biocontainers/i2nca:0.3.12_cv1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{githubi2nca,
+ author = {Jannik Witte},
+ title = {i2nca},
+ publisher = {GitHub},
+ journal = {Github repository},
+ url = {https://github.com/cKNUSPeR/i2nca}
+ }
+
+
+ @article{10.1093/gigascience/giab049,
+ author = {Cordes, Jonas and Enzlein, Thomas and Marsching, Christian and Hinze, Marven and Engelhardt, Sandy and Hopf, Carsten and Wolf, Ivo},
+ title = "{M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data}",
+ journal = {GigaScience},
+ volume = {10},
+ number = {7},
+ year = {2021},
+ month = {07},
+ issn = {2047-217X},
+ doi = {10.1093/gigascience/giab049},
+ url = {https://doi.org/10.1093/gigascience/giab049}
+ }
+
+
+
\ No newline at end of file
diff --git a/tools/i2nca/i2nca_calibrant_qc.xml b/tools/i2nca/i2nca_calibrant_qc.xml
new file mode 100644
index 000000000..c1f68a28c
--- /dev/null
+++ b/tools/i2nca/i2nca_calibrant_qc.xml
@@ -0,0 +1,135 @@
+
+
+
+ Create a Calibrant Quality control reports for any kind of .imzML file.
+ Supply a csv file with Signals to visualize them and their accuracies
+ Different metrics will be visualized as a pdf report.
+
+
+
+ macros.xml
+
+
+
+ biocontainers/i2nca:0.3.12_cv1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{githubi2nca,
+ author = {Jannik Witte},
+ title = {i2nca},
+ publisher = {GitHub},
+ journal = {Github repository},
+ url = {https://github.com/cKNUSPeR/i2nca}
+ }
+
+
+ @article{10.1093/gigascience/giab049,
+ author = {Cordes, Jonas and Enzlein, Thomas and Marsching, Christian and Hinze, Marven and Engelhardt, Sandy and Hopf, Carsten and Wolf, Ivo},
+ title = "{M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data}",
+ journal = {GigaScience},
+ volume = {10},
+ number = {7},
+ year = {2021},
+ month = {07},
+ issn = {2047-217X},
+ doi = {10.1093/gigascience/giab049},
+ url = {https://doi.org/10.1093/gigascience/giab049}
+ }
+
+
+
\ No newline at end of file
diff --git a/tools/i2nca/i2nca_cp_2_pc.xml b/tools/i2nca/i2nca_cp_2_pc.xml
new file mode 100644
index 000000000..618d28acd
--- /dev/null
+++ b/tools/i2nca/i2nca_cp_2_pc.xml
@@ -0,0 +1,364 @@
+
+
+
+ Convert profile imzML files with i2nca and m2aia to obtain processed centroid files.
+
+
+
+
+ macros.xml
+
+
+
+ biocontainers/i2nca:0.3.12_cv1
+
+
+
+ $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #else if $m2aia.use_m2aia_preproc == "TRUE":
+ 'i2nca_convert_to_pc' 'indata.imzML' './outdata' '$choose_strategy.strategy' '--fp_hei' '$choose_strategy.fp_hei' '--fp_dis' '$choose_strategy.fp_dis' '--fp_pro' '$choose_strategy.fp_pro' '--fp_thr' '$choose_strategy.fp_thr' '--fp_wid' '$choose_strategy.fp_wid' '--fp_wlen' '$choose_strategy.fp_wlen' '--fp_rhei' '$choose_strategy.fp_rhei' '--fp_pla' '$choose_strategy.fp_pla' @M2AIA_PARAMETERS@ &&
+
+ mkdir $outfile_imzml.files_path &&
+
+ mv ./outdata_conv_output_proc_centroid.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_proc_centroid.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #end if
+ #end if
+
+ #if $choose_strategy.strategy == "set_find_peaks_simple":
+
+ #if $m2aia.use_m2aia_preproc == "FALSE":
+ 'i2nca_convert_to_pc' 'indata.imzML' './outdata' '$choose_strategy.strategy' '--fp_hei' '$choose_strategy.fp_hei' '--fp_pro' '$choose_strategy.fp_pro' &&
+
+ mkdir $outfile_imzml.files_path &&
+
+ mv ./outdata_conv_output_proc_centroid.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_proc_centroid.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #else if $m2aia.use_m2aia_preproc == "TRUE":
+ 'i2nca_convert_to_pc' 'indata.imzML' './outdata' '$choose_strategy.strategy' '--fp_hei' '$choose_strategy.fp_hei' '--fp_pro' '$choose_strategy.fp_pro' @M2AIA_PARAMETERS@ &&
+
+ mkdir $outfile_imzml.files_path &&
+
+ mv ./outdata_conv_output_proc_centroid.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_proc_centroid.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #end if
+ #end if
+
+ #if $choose_strategy.strategy == "set_find_peaks_cwt":
+ #if $m2aia.use_m2aia_preproc == "FALSE":
+
+ 'i2nca_convert_to_pc' 'indata.imzML' './outdata' '$choose_strategy.strategy' '--cwt_wid' '$choose_strategy.cwt_wid' '--cwt_snr' '$choose_strategy.cwt_snr' '--cwt_nper' '$choose_strategy.cwt_nper' '--cwt_win' '$choose_strategy.cwt_win' &&
+
+ mkdir $outfile_imzml.files_path &&
+
+ mv ./outdata_conv_output_proc_centroid.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_proc_centroid.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #else if $m2aia.use_m2aia_preproc == "TRUE":
+
+ 'i2nca_convert_to_pc' 'indata.imzML' './outdata' '$choose_strategy.strategy' '--cwt_wid' '$choose_strategy.cwt_wid' '--cwt_snr' '$choose_strategy.cwt_snr' '--cwt_nper' '$choose_strategy.cwt_nper' '--cwt_win' '$choose_strategy.cwt_win' @M2AIA_PARAMETERS@ &&
+
+ mkdir $outfile_imzml.files_path &&
+
+ mv ./outdata_conv_output_proc_centroid.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_proc_centroid.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+ #end if
+ #end if
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{githubi2nca,
+ author = {Jannik Witte},
+ title = {i2nca},
+ publisher = {GitHub},
+ journal = {Github repository},
+ url = {https://github.com/cKNUSPeR/i2nca}
+ }
+
+
+ @article{10.1093/gigascience/giab049,
+ author = {Cordes, Jonas and Enzlein, Thomas and Marsching, Christian and Hinze, Marven and Engelhardt, Sandy and Hopf, Carsten and Wolf, Ivo},
+ title = "{M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data}",
+ journal = {GigaScience},
+ volume = {10},
+ number = {7},
+ year = {2021},
+ month = {07},
+ issn = {2047-217X},
+ doi = {10.1093/gigascience/giab049},
+ url = {https://doi.org/10.1093/gigascience/giab049}
+ }
+
+
+ @article{10.1093/bioinformatics/btl355,
+ author = {Du, Pan and Kibbe, Warren A. and Lin, Simon M.},
+ title = "{Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching}",
+ journal = {Bioinformatics},
+ volume = {22},
+ number = {17},
+ pages = {2059-2065},
+ year = {2006},
+ month = {07},issn = {1367-4803},
+ doi = {10.1093/bioinformatics/btl355},
+ url = {https://doi.org/10.1093/bioinformatics/btl355},
+ }
+
+
+
diff --git a/tools/i2nca/i2nca_file_cutter.xml b/tools/i2nca/i2nca_file_cutter.xml
new file mode 100644
index 000000000..2e0854876
--- /dev/null
+++ b/tools/i2nca/i2nca_file_cutter.xml
@@ -0,0 +1,109 @@
+
+
+
+ Split an imzML file into different smaller flies based on a ROI annoation.
+
+
+
+ macros.xml
+
+
+
+ biocontainers/i2nca:0.3.12_cv1
+
+
+
+ $outfile_a &&
+ ls -l "$outfile_a.files_path" >> $outfile_a &&
+
+ echo "imzML B:" > $outfile_b &&
+ ls -l "$outfile_b.files_path" >> $outfile_b
+
+ ## currently, only the first two files are returned, as the dynamic collecting fails
+
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{githubi2nca,
+ author = {Jannik Witte},
+ title = {i2nca},
+ publisher = {GitHub},
+ journal = {Github repository},
+ url = {https://github.com/cKNUSPeR/i2nca}
+ }
+
+
+ @article{10.1093/gigascience/giab049,
+ author = {Cordes, Jonas and Enzlein, Thomas and Marsching, Christian and Hinze, Marven and Engelhardt, Sandy and Hopf, Carsten and Wolf, Ivo},
+ title = "{M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data}",
+ journal = {GigaScience},
+ volume = {10},
+ number = {7},
+ year = {2021},
+ month = {07},
+ issn = {2047-217X},
+ doi = {10.1093/gigascience/giab049},
+ url = {https://doi.org/10.1093/gigascience/giab049}
+ }
+
+
+
+
\ No newline at end of file
diff --git a/tools/i2nca/i2nca_file_joiner.xml b/tools/i2nca/i2nca_file_joiner.xml
new file mode 100644
index 000000000..be57f62b3
--- /dev/null
+++ b/tools/i2nca/i2nca_file_joiner.xml
@@ -0,0 +1,167 @@
+
+
+
+ Combine two or more .imzML files together to one file.
+ Geometry and location of all files can be controlled.
+ It is recommended to perform a normalization before joining.
+ The resulting file will be a processed file.
+
+
+
+ macros.xml
+
+
+
+ biocontainers/i2nca:0.3.12_cv1
+
+
+ $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{githubi2nca,
+ author = {Jannik Witte},
+ title = {i2nca},
+ publisher = {GitHub},
+ journal = {Github repository},
+ url = {https://github.com/cKNUSPeR/i2nca}
+ }
+
+
+ @article{10.1093/gigascience/giab049,
+ author = {Cordes, Jonas and Enzlein, Thomas and Marsching, Christian and Hinze, Marven and Engelhardt, Sandy and Hopf, Carsten and Wolf, Ivo},
+ title = "{M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data}",
+ journal = {GigaScience},
+ volume = {10},
+ number = {7},
+ year = {2021},
+ month = {07},
+ issn = {2047-217X},
+ doi = {10.1093/gigascience/giab049},
+ url = {https://doi.org/10.1093/gigascience/giab049}
+ }
+
+
+
\ No newline at end of file
diff --git a/tools/i2nca/i2nca_pc_2_cc.xml b/tools/i2nca/i2nca_pc_2_cc.xml
new file mode 100644
index 000000000..fe9c152aa
--- /dev/null
+++ b/tools/i2nca/i2nca_pc_2_cc.xml
@@ -0,0 +1,240 @@
+
+
+
+ Convert centroid imzML files with i2nca and m2aia to obtain ContinuousCentroid files.
+
+
+
+
+ macros.xml
+
+
+
+ biocontainers/i2nca:0.3.12_cv1
+
+
+ $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #else if $m2aia.use_m2aia_preproc == "TRUE":
+ 'i2nca_convert_to_cc' 'indata.imzML' './outdata' '$choose_strategy.strategy' '--acc' '$choose_strategy.value' @M2AIA_PARAMETERS@ &&
+
+ mkdir $outfile_imzml.files_path &&
+
+ mv ./outdata_conv_output_cont_centroid.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_cont_centroid.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #end if
+ #end if
+ #if $choose_strategy.strategy == "unique":
+ #if $m2aia.use_m2aia_preproc == "FALSE":
+ 'i2nca_convert_to_cc' 'indata.imzML' './outdata' '$choose_strategy.strategy' &&
+
+ mkdir $outfile_imzml.files_path &&
+
+ mv ./outdata_conv_output_cont_centroid.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_cont_centroid.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #else if $m2aia.use_m2aia_preproc == "TRUE":
+
+ 'i2nca_convert_to_cc' 'indata.imzML' './outdata' '$choose_strategy.strategy' @M2AIA_PARAMETERS@ &&
+
+ mkdir $outfile_imzml.files_path &&
+
+ mv ./outdata_conv_output_cont_centroid.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_cont_centroid.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+ #end if
+ #end if
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ -->
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{githubi2nca,
+ author = {Jannik Witte},
+ title = {i2nca},
+ publisher = {GitHub},
+ journal = {Github repository},
+ url = {https://github.com/cKNUSPeR/i2nca}
+ }
+
+
+ @article{10.1093/gigascience/giab049,
+ author = {Cordes, Jonas and Enzlein, Thomas and Marsching, Christian and Hinze, Marven and Engelhardt, Sandy and Hopf, Carsten and Wolf, Ivo},
+ title = "{M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data}",
+ journal = {GigaScience},
+ volume = {10},
+ number = {7},
+ year = {2021},
+ month = {07},
+ issn = {2047-217X},
+ doi = {10.1093/gigascience/giab049},
+ url = {https://doi.org/10.1093/gigascience/giab049}
+ }
+
+
+
diff --git a/tools/i2nca/i2nca_pp_2_cp.xml b/tools/i2nca/i2nca_pp_2_cp.xml
new file mode 100644
index 000000000..4e346ece9
--- /dev/null
+++ b/tools/i2nca/i2nca_pp_2_cp.xml
@@ -0,0 +1,226 @@
+
+
+
+ Convert ProcessedProfile imzML files with i2nca and m2aia to obtain ContinuousProfile imzML files.
+
+
+
+
+ macros.xml
+
+
+
+ biocontainers/i2nca:0.3.12_cv1
+
+
+
+ $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #else if $m2aia.use_m2aia_preproc == "TRUE":
+ 'i2nca_convert_to_cp' '--cov' '${choose_strategy.value}' 'indata.imzML' './outdata' '$choose_strategy.strategy' @M2AIA_PARAMETERS@ &&
+
+ mkdir $outfile_imzml.files_path &&
+ mv ./outdata_conv_output_cont_profile.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_cont_profile.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #end if
+ #end if
+ #if $choose_strategy.strategy == "fixed_binning":
+ #if $m2aia.use_m2aia_preproc == "FALSE":
+ 'i2nca_convert_to_cp' '--acc' '${choose_strategy.value}' 'indata.imzML' './outdata' '$choose_strategy.strategy' &&
+
+ mkdir $outfile_imzml.files_path &&
+ mv ./outdata_conv_output_cont_profile.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_cont_profile.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #else if $m2aia.use_m2aia_preproc == "TRUE":
+ 'i2nca_convert_to_cp' '--acc' '${choose_strategy.value}' 'indata.imzML' './outdata' '$choose_strategy.strategy' @M2AIA_PARAMETERS@ &&
+ mkdir $outfile_imzml.files_path &&
+ mv ./outdata_conv_output_cont_profile.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
+ mv ./outdata_conv_output_cont_profile.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
+
+ echo "imzML file:" > $outfile_imzml &&
+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml
+
+ #end if
+ #end if
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{githubi2nca,
+ author = {Jannik Witte},
+ title = {i2nca},
+ publisher = {GitHub},
+ journal = {Github repository},
+ url = {https://github.com/cKNUSPeR/i2nca}
+ }
+
+
+ @article{10.1093/gigascience/giab049,
+ author = {Cordes, Jonas and Enzlein, Thomas and Marsching, Christian and Hinze, Marven and Engelhardt, Sandy and Hopf, Carsten and Wolf, Ivo},
+ title = "{M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data}",
+ journal = {GigaScience},
+ volume = {10},
+ number = {7},
+ year = {2021},
+ month = {07},
+ issn = {2047-217X},
+ doi = {10.1093/gigascience/giab049},
+ url = {https://doi.org/10.1093/gigascience/giab049}
+ }
+
+
+
diff --git a/tools/i2nca/i2nca_region_qc.xml b/tools/i2nca/i2nca_region_qc.xml
new file mode 100644
index 000000000..f546082c4
--- /dev/null
+++ b/tools/i2nca/i2nca_region_qc.xml
@@ -0,0 +1,126 @@
+
+
+
+ Create a Quality Control report for different Regions of Interest (ROI) for any kind of .imzML file.
+ Supply a tsv file with x and y annotation for the regions.
+ Different metrics will be visualized as a pdf report.
+
+
+
+ macros.xml
+
+
+
+ biocontainers/i2nca:0.3.12_cv1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ with_tsv_annotation['add'] == "No"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{githubi2nca,
+ author = {Jannik Witte},
+ title = {i2nca},
+ publisher = {GitHub},
+ journal = {Github repository},
+ url = {https://github.com/cKNUSPeR/i2nca}
+ }
+
+
+ @article{10.1093/gigascience/giab049,
+ author = {Cordes, Jonas and Enzlein, Thomas and Marsching, Christian and Hinze, Marven and Engelhardt, Sandy and Hopf, Carsten and Wolf, Ivo},
+ title = "{M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data}",
+ journal = {GigaScience},
+ volume = {10},
+ number = {7},
+ year = {2021},
+ month = {07},
+ issn = {2047-217X},
+ doi = {10.1093/gigascience/giab049},
+ url = {https://doi.org/10.1093/gigascience/giab049}
+ }
+
+
+
\ No newline at end of file
diff --git a/tools/i2nca/macros.xml b/tools/i2nca/macros.xml
new file mode 100644
index 000000000..81254acf7
--- /dev/null
+++ b/tools/i2nca/macros.xml
@@ -0,0 +1,122 @@
+
+ 0.1.0
+ 0
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ '--nor' '${m2aia.nor}' '--itr' '${m2aia.itr}' '--bsl_hws' '${m2aia.bsl_hws}' '--bsl' '${m2aia.bsl}' '--smo_hws' '${m2aia.smo_hws}' '--smo' '${m2aia.smo}'
+
+ `_
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+
diff --git a/tools/i2nca/test-data/Agnostic_QC_Report_CC.pdf b/tools/i2nca/test-data/Agnostic_QC_Report_CC.pdf
new file mode 100644
index 000000000..085e18d69
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diff --git a/tools/i2nca/test-data/Agnostic_QC_Report_CP.pdf b/tools/i2nca/test-data/Agnostic_QC_Report_CP.pdf
new file mode 100644
index 000000000..1d6337682
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diff --git a/tools/i2nca/test-data/Agnostic_QC_Report_PC.pdf b/tools/i2nca/test-data/Agnostic_QC_Report_PC.pdf
new file mode 100644
index 000000000..75996fe7a
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diff --git a/tools/i2nca/test-data/Agnostic_QC_Report_PP.pdf b/tools/i2nca/test-data/Agnostic_QC_Report_PP.pdf
new file mode 100644
index 000000000..5c207830e
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diff --git a/tools/i2nca/test-data/Agnostic_QC_Report_jPC.pdf b/tools/i2nca/test-data/Agnostic_QC_Report_jPC.pdf
new file mode 100644
index 000000000..60ee712fc
Binary files /dev/null and b/tools/i2nca/test-data/Agnostic_QC_Report_jPC.pdf differ
diff --git a/tools/i2nca/test-data/AutoROI_Annotation_PC.tsv b/tools/i2nca/test-data/AutoROI_Annotation_PC.tsv
new file mode 100644
index 000000000..0d2175ced
--- /dev/null
+++ b/tools/i2nca/test-data/AutoROI_Annotation_PC.tsv
@@ -0,0 +1,5 @@
+x y annotation
+0 0 1
+1 0 1
+2 0 1
+3 0 1
diff --git a/tools/i2nca/test-data/Calibrant_QC_Report_CC.pdf b/tools/i2nca/test-data/Calibrant_QC_Report_CC.pdf
new file mode 100644
index 000000000..7f075efcf
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diff --git a/tools/i2nca/test-data/Calibrant_QC_Report_CP.pdf b/tools/i2nca/test-data/Calibrant_QC_Report_CP.pdf
new file mode 100644
index 000000000..047be89e0
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diff --git a/tools/i2nca/test-data/Calibrant_QC_Report_PC.pdf b/tools/i2nca/test-data/Calibrant_QC_Report_PC.pdf
new file mode 100644
index 000000000..a5c563034
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diff --git a/tools/i2nca/test-data/Calibrant_QC_Report_PP.pdf b/tools/i2nca/test-data/Calibrant_QC_Report_PP.pdf
new file mode 100644
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diff --git a/tools/i2nca/test-data/Calibrant_QC_Report_jPC.pdf b/tools/i2nca/test-data/Calibrant_QC_Report_jPC.pdf
new file mode 100644
index 000000000..a428d68c4
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diff --git a/tools/i2nca/test-data/Region_QC_Report_CP.pdf b/tools/i2nca/test-data/Region_QC_Report_CP.pdf
new file mode 100644
index 000000000..d603b9f4b
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diff --git a/tools/i2nca/test-data/Region_QC_Report_PC.pdf b/tools/i2nca/test-data/Region_QC_Report_PC.pdf
new file mode 100644
index 000000000..975b69745
Binary files /dev/null and b/tools/i2nca/test-data/Region_QC_Report_PC.pdf differ
diff --git a/tools/i2nca/test-data/calibrant.csv b/tools/i2nca/test-data/calibrant.csv
new file mode 100644
index 000000000..c8299e64a
--- /dev/null
+++ b/tools/i2nca/test-data/calibrant.csv
@@ -0,0 +1,5 @@
+mz;name;comment
+78.959;Calibrant A; in all pixel
+134.862;Calibrant B; in pixel 2
+222.222;Calibrant C; no signal
+500.00;CalibrantD; out of mz range
\ No newline at end of file
diff --git a/tools/i2nca/test-data/cc.ibd b/tools/i2nca/test-data/cc.ibd
new file mode 100644
index 000000000..61ba8fbe5
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diff --git a/tools/i2nca/test-data/cc.imzML b/tools/i2nca/test-data/cc.imzML
new file mode 100644
index 000000000..87304a76a
--- /dev/null
+++ b/tools/i2nca/test-data/cc.imzML
@@ -0,0 +1,210 @@
+
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diff --git a/tools/i2nca/test-data/combined_pc.ibd b/tools/i2nca/test-data/combined_pc.ibd
new file mode 100644
index 000000000..45740e604
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diff --git a/tools/i2nca/test-data/combined_pc.imzML b/tools/i2nca/test-data/combined_pc.imzML
new file mode 100644
index 000000000..b0d61e843
--- /dev/null
+++ b/tools/i2nca/test-data/combined_pc.imzML
@@ -0,0 +1,338 @@
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diff --git a/tools/i2nca/test-data/combined_pc_roi.tsv b/tools/i2nca/test-data/combined_pc_roi.tsv
new file mode 100644
index 000000000..e6287d5ad
--- /dev/null
+++ b/tools/i2nca/test-data/combined_pc_roi.tsv
@@ -0,0 +1,9 @@
+x y annotation
+0 0 A
+1 0 A
+2 0 A
+3 0 A
+0 20 B
+1 20 B
+2 20 B
+3 20 B
diff --git a/tools/i2nca/test-data/cp.ibd b/tools/i2nca/test-data/cp.ibd
new file mode 100644
index 000000000..3638c882e
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diff --git a/tools/i2nca/test-data/cp.imzML b/tools/i2nca/test-data/cp.imzML
new file mode 100644
index 000000000..c7d5f8b89
--- /dev/null
+++ b/tools/i2nca/test-data/cp.imzML
@@ -0,0 +1,210 @@
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diff --git a/tools/i2nca/test-data/cp_test1.ibd b/tools/i2nca/test-data/cp_test1.ibd
new file mode 100644
index 000000000..59cda2dfe
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diff --git a/tools/i2nca/test-data/cp_test1.imzml b/tools/i2nca/test-data/cp_test1.imzml
new file mode 100644
index 000000000..27be79980
--- /dev/null
+++ b/tools/i2nca/test-data/cp_test1.imzml
@@ -0,0 +1,210 @@
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diff --git a/tools/i2nca/test-data/cp_test2.ibd b/tools/i2nca/test-data/cp_test2.ibd
new file mode 100644
index 000000000..efa6acd31
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diff --git a/tools/i2nca/test-data/cp_test2.imzml b/tools/i2nca/test-data/cp_test2.imzml
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diff --git a/tools/i2nca/test-data/cp_test3.ibd b/tools/i2nca/test-data/cp_test3.ibd
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diff --git a/tools/i2nca/test-data/cp_test4.ibd b/tools/i2nca/test-data/cp_test4.ibd
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diff --git a/tools/i2nca/test-data/cp_test5.ibd b/tools/i2nca/test-data/cp_test5.ibd
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diff --git a/tools/i2nca/test-data/cp_test5.imzml b/tools/i2nca/test-data/cp_test5.imzml
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diff --git a/tools/i2nca/test-data/cp_test6.ibd b/tools/i2nca/test-data/cp_test6.ibd
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diff --git a/tools/i2nca/test-data/jpc_test1.ibd b/tools/i2nca/test-data/jpc_test1.ibd
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diff --git a/tools/i2nca/test-data/jpc_test1.imzml b/tools/i2nca/test-data/jpc_test1.imzml
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diff --git a/tools/i2nca/test-data/jpc_test1_annotation.tsv b/tools/i2nca/test-data/jpc_test1_annotation.tsv
new file mode 100644
index 000000000..2834b0daa
--- /dev/null
+++ b/tools/i2nca/test-data/jpc_test1_annotation.tsv
@@ -0,0 +1,9 @@
+old_x old_y old_file new_x new_y
+0 0 indata_1.imzML 1 1
+1 0 indata_1.imzML 2 1
+2 0 indata_1.imzML 3 1
+3 0 indata_1.imzML 4 1
+0 0 indata_2.imzML 14 1
+1 0 indata_2.imzML 15 1
+2 0 indata_2.imzML 16 1
+3 0 indata_2.imzML 17 1
diff --git a/tools/i2nca/test-data/pc.ibd b/tools/i2nca/test-data/pc.ibd
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diff --git a/tools/i2nca/test-data/pc.imzML b/tools/i2nca/test-data/pc.imzML
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diff --git a/tools/i2nca/test-data/pc_test1.ibd b/tools/i2nca/test-data/pc_test1.ibd
new file mode 100644
index 000000000..e5f63a1a8
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diff --git a/tools/i2nca/test-data/pc_test1.imzml b/tools/i2nca/test-data/pc_test1.imzml
new file mode 100644
index 000000000..3e860944f
--- /dev/null
+++ b/tools/i2nca/test-data/pc_test1.imzml
@@ -0,0 +1,210 @@
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diff --git a/tools/i2nca/test-data/pc_test2.ibd b/tools/i2nca/test-data/pc_test2.ibd
new file mode 100644
index 000000000..e3115ed04
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diff --git a/tools/i2nca/test-data/pc_test2.imzml b/tools/i2nca/test-data/pc_test2.imzml
new file mode 100644
index 000000000..bab06a9d0
--- /dev/null
+++ b/tools/i2nca/test-data/pc_test2.imzml
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diff --git a/tools/i2nca/test-data/pc_test3.ibd b/tools/i2nca/test-data/pc_test3.ibd
new file mode 100644
index 000000000..271b61f4d
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diff --git a/tools/i2nca/test-data/pc_test3.imzml b/tools/i2nca/test-data/pc_test3.imzml
new file mode 100644
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diff --git a/tools/i2nca/test-data/pc_test4.ibd b/tools/i2nca/test-data/pc_test4.ibd
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diff --git a/tools/i2nca/test-data/pc_test4.imzml b/tools/i2nca/test-data/pc_test4.imzml
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diff --git a/tools/i2nca/test-data/pc_test5.ibd b/tools/i2nca/test-data/pc_test5.ibd
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diff --git a/tools/i2nca/test-data/pp.ibd b/tools/i2nca/test-data/pp.ibd
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diff --git a/tools/i2nca/test-data/pp_test1.ibd b/tools/i2nca/test-data/pp_test1.ibd
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diff --git a/tools/i2nca/test-data/pp_test2.ibd b/tools/i2nca/test-data/pp_test2.ibd
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diff --git a/tools/i2nca/test-data/pp_test2.imzml b/tools/i2nca/test-data/pp_test2.imzml
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diff --git a/tools/i2nca/test-data/pp_test3.ibd b/tools/i2nca/test-data/pp_test3.ibd
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diff --git a/tools/i2nca/test-data/pp_test3.imzml b/tools/i2nca/test-data/pp_test3.imzml
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diff --git a/tools/i2nca/test-data/pp_test4.ibd b/tools/i2nca/test-data/pp_test4.ibd
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diff --git a/tools/i2nca/test-data/pp_test4.imzml b/tools/i2nca/test-data/pp_test4.imzml
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diff --git a/tools/i2nca/test-data/regions.tsv b/tools/i2nca/test-data/regions.tsv
new file mode 100644
index 000000000..d8798708f
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+x y annotation
+0 0 1
+1 0 2
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+3 0 3