Initial commit for i2nca

pythonProject/main.py

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+# 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/

tools/i2nca/.shed.yml

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+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

tools/i2nca/i2nca_agnostic_qc.xml

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+<tool id="i2nca_agnostic_qc" name="i2nca Agnostic QC Report " version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+
+	<description>
+        Create agnostic quality control reports for any kind of .imzML file.
+        Different metrics will be visualized as a pdf report. 
+    </description>
+
+    <macros>
+    <import>macros.xml</import>
+    </macros>
+
+    <requirements>
+        <container type="docker">biocontainers/i2nca:0.3.12_cv1</container>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+    cp "${infile.extra_files_path}/imzml" indata.imzML &&
+    cp "${infile.extra_files_path}/ibd" indata.ibd &&
+    i2nca_agnostic_qc 'indata.imzML' './data' 
+    ]]></command>
+
+    <inputs>
+        <param name="infile" type="data" format="imzml" label="MSI data" help="Load the .imzml file on which the QC should be performed"/>
+    </inputs>
+
+    <outputs>
+            <data name="AgnosticQC" label="Agnostic QC report on ${on_string}" from_work_dir="data_agnostic_QC.pdf" format="pdf" />
+    </outputs>
+
+    <tests>
+        <!-- Test 1: QC on pp-->
+        <test>
+            <expand macro="pp_infile"/>
+            <output name="AgnosticQC" file="Agnostic_QC_Report_PP.pdf" compare="sim_size"/>
+        </test>
+
+        <!-- Test 2: QC on cc-->
+        <test>
+            <expand macro="cc_infile"/>
+            <output name="AgnosticQC" file="Agnostic_QC_Report_CC.pdf" compare="sim_size"/>
+        </test>
+
+        <!-- Test 3: QC on cp-->
+        <test>
+            <expand macro="cp_infile"/>
+            <output name="AgnosticQC" file="Agnostic_QC_Report_CP.pdf" compare="sim_size"/>
+        </test>
+
+        <!-- Test 4: QC on pc-->
+        <test>
+            <expand macro="pc_infile"/>
+            <output name="AgnosticQC" file="Agnostic_QC_Report_PC.pdf" compare="sim_size"/>
+        </test>
+
+        <!-- Test 45: QC on jpc-->
+        <test>
+            <expand macro="jpc_infile"/>
+            <output name="AgnosticQC" file="Agnostic_QC_Report_jPC.pdf" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        @I2NCA_DESCRIPTION@
+
+        This tool performs a quality control report generation on any imzml file. 
+        In the report, different metrics will be visualized. This report doesn't require any input other that a dataset.
+        cool, with docker help
+
+        **Input data**
+
+
+        @MSIDATA_INPUT_DESCRIPTION@
+
+        ]]></help>
+        <citations>
+            <citation type="bibtex">
+                @misc{githubi2nca,
+                author = {Jannik Witte},
+                title = {i2nca},
+                publisher = {GitHub},
+                journal = {Github repository},
+                url = {https://github.com/cKNUSPeR/i2nca}
+            }
+            </citation>
+            <citation type="bibtex">
+                @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}
+                }
+            </citation>
+        </citations>
+</tool>

tools/i2nca/i2nca_calibrant_qc.xml

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+<tool id="i2nca_calibrant_qc" name="i2nca Calibrant QC Report" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+
+	<description>
+        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.
+    </description>
+
+    <macros>
+    <import>macros.xml</import>
+    </macros>
+
+    <requirements>
+        <container type="docker">biocontainers/i2nca:0.3.12_cv1</container>
+    </requirements>
+
+
+    <command detect_errors="exit_code"><![CDATA[
+    cp "${infile.extra_files_path}/imzml" indata.imzML &&
+    cp "${infile.extra_files_path}/ibd" indata.ibd &&
+    'i2nca_calibrant_qc' 'indata.imzML' './data' '$csv_annotation' --ppm '$ppm' --sample_size '$subsample'
+    ]]></command>
+
+    <inputs>
+        <param name="infile" type="data" format="imzml" label="MSI data" help="Load the imzML file (as Composite) on which the QC should be performed"/>
+        <param name="csv_annotation" label="Input csv file with signal annotation" type="data" format="csv" help="Load an .csv file for theoretical signals on which the QC should be performed.
+        Please use ';' as delimiter. The columns with the signals must be named 'name' and the respecive thoeretical m/z value must be named 'mz'" />
+        <param name="ppm" value="50" type="integer" label="ppm range (plusminus)" help="Cutoff on accuracy in ppm.
+        Determines the interval around the theoretical signal that is still considered in the report."/>
+        <param name="subsample" value="0.05" type="float" label="Subsample Percentage" help="Subset percentage of the file that is used in the raw data overview."/>
+    </inputs>
+
+
+    <outputs>
+            <data name="CalibrantQC" label="Calibrant QC report on ${on_string}" from_work_dir="data_calibrant_QC.pdf" format="pdf" />
+    </outputs>
+
+
+    <tests>
+        <!-- Test 1: QC on pp-->
+        <test>
+            <expand macro="pp_infile"/>
+            <param name="csv_annotation" value="calibrant.csv" ftype="csv"/>
+            <param name="ppm" value="50" />
+            <param name="subsample" value="1.0"/>
+            <output name="CalibrantQC" file="Calibrant_QC_Report_PP.pdf" compare="sim_size"/>
+        </test>
+
+        <!-- Test 2: QC on cc-->
+        <test>
+            <expand macro="cc_infile"/>
+            <param name="csv_annotation" value="calibrant.csv" ftype="csv"/>
+            <param name="ppm" value="50" />
+            <param name="subsample" value="1.0"/>
+            <output name="CalibrantQC" file="Calibrant_QC_Report_CC.pdf" compare="sim_size"/>
+        </test>
+
+        <!-- Test 3: QC on cp-->
+        <test>
+            <expand macro="cp_infile"/>
+            <param name="csv_annotation" value="calibrant.csv" ftype="csv"/>
+            <param name="ppm" value="50" />
+            <param name="subsample" value="1.0"/>
+            <output name="CalibrantQC" file="Calibrant_QC_Report_CP.pdf" compare="sim_size"/>
+        </test>
+
+        <!-- Test 4: QC on pc-->
+        <test>
+            <expand macro="pc_infile"/>
+            <param name="csv_annotation" value="calibrant.csv" ftype="csv"/>
+            <param name="ppm" value="50" />
+            <param name="subsample" value="1.0"/>
+            <output name="CalibrantQC" file="Calibrant_QC_Report_PC.pdf" compare="sim_size"/>
+        </test>
+
+        <!-- Test 45: QC on jpc-->
+        <test>
+            <expand macro="jpc_infile"/>
+            <param name="csv_annotation" value="calibrant.csv" ftype="csv"/>
+            <param name="ppm" value="50" />
+            <param name="subsample" value="1.0"/>
+            <output name="CalibrantQC" file="Calibrant_QC_Report_jPC.pdf" compare="sim_size"/>
+        </test>
+    </tests>
+
+
+    <help><![CDATA[
+        @I2NCA_DESCRIPTION@
+
+        This tool performs a quality control report generation on any imzml file. 
+        In the report, different metrics will be visualized. This report doesn't require any input other that a dataset.
+
+        **Input data**
+
+
+        @MSIDATA_INPUT_DESCRIPTION@
+
+        Signal annotation: Please provide a list of m/z values of interest as csv file with ";" delimiter:
+        - The column with a unique identifier for each mass of interest must be called "name".
+        - The m/z value of interest must be provided as "mz".
+        - The annotation file may contain any additional columns.
+
+        ppm range: Provide the half-interval around the m/z values of interest where peaks are still considered part of the signal.
+
+        subsample percentage: Set the percentage of pixels that are utilized for visualization. Changing this number helps adjust the readability of some graphs in the report.
+
+
+
+        ]]></help>
+        <citations>
+            <citation type="bibtex">
+                @misc{githubi2nca,
+                author = {Jannik Witte},
+                title = {i2nca},
+                publisher = {GitHub},
+                journal = {Github repository},
+                url = {https://github.com/cKNUSPeR/i2nca}
+            }
+            </citation>
+            <citation type="bibtex">
+                @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}
+                }
+            </citation>
+        </citations>
+</tool>