Added XCMS plotting tools (#267)

Added XCMS plotting tools --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> Co-authored-by: Zargham Ahmad <zargham.ahmad12@gmail.com>
workflow4metabolomics · Jul 15, 2024 · eca29d4 · eca29d4
1 parent eba1150
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diff --git a/tools/xcms/.shed.yml b/tools/xcms/.shed.yml
@@ -111,7 +111,38 @@ repositories:
     owner: lecorguille
     include:
       [*default-includes, msnbase_readmsdata.xml, msnbase_readmsdata.r, macros_msnbase.xml]
-
+  xcms_plot_raw:
+    description: Plot raw mzml file content with xcms
+    long_description: |
+      This suite provides tools from the XCMS package to visualize extracted ion chromatograms and raw data 
+      from a single mzML file. Users can define m/z and retention time (rt) values, and the suite plots data 
+      with a user-defined tolerance and rt range centered around the selected m/z and rt values.
+      The MsExperiment plot function creates a two-dimensional view of three-dimensional mass spectrometry data,
+      displaying peaks in the two-dimensional m/z versus retention time plane with intensity color-coding. The plot
+      is saved as a PNG file
+    owner: workflow4metabolomics
+    type: unrestricted
+    include:
+      - xcms_plot_raw.xml
+      - macros_xcms_plot.xml
+      - test-data/raw_plot.png
+      - test-data/xcms_plot_raw_testdata.mzML
+  xcms_plot_eic:
+    description: Plot EIC using xcms
+    long_description: |
+      This suite provides tools from the XCMS package to visualize extracted ion chromatograms and raw data 
+      from a single mzML file. Users can define m/z and retention time (rt) values, and the suite plots data 
+      with a user-defined tolerance and rt range centered around the selected m/z and rt values.
+      The MsExperiment plot function creates a two-dimensional view of three-dimensional mass spectrometry data,
+      displaying peaks in the two-dimensional m/z versus retention time plane with intensity color-coding. The plot
+      is saved as a PNG file
+    owner: workflow4metabolomics
+    type: unrestricted
+    include:
+      - xcms_plot_eic.xml
+      - macros_xcms_plot.xml
+      - test-data/eic_plot.png
+      - test-data/xcms_plot_eic_testdata.mzML
 suite:
   name: suite_xcms
   owner: lecorguille
@@ -122,3 +153,5 @@ suite:
     http://www.bioconductor.org/packages/release/bioc/html/xcms.html
     XCMS: processing mass spectrometry data for metabolite profiling
     using nonlinear peak alignment, matching, and identification
+
+
diff --git a/tools/xcms/macros_xcms_plot.xml b/tools/xcms/macros_xcms_plot.xml
@@ -0,0 +1,38 @@
+<macros>
+    <token name="@TOOL_VERSION@">4.0.0</token>
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Wudmir"
+                familyName="Rojas"
+                url="https://github.com/wverastegui"
+                identifier="0000-0001-7036-9987" />
+            <person
+                givenName="Helge"
+                familyName="Hecht"
+                url="https://github.com/hechth"
+                identifier="0000-0001-6744-996X" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+                name="RECETOX MUNI"/>
+        </creator>
+    </xml>
+    <xml name="bio.tools">
+        <xrefs>
+            <xref type="bio.tools">XCMS</xref>
+        </xrefs>
+    </xml>
+    <xml name="base_params">
+        <param type="data" name="input" format="mzML" label="Input mzML file"/>
+        <param type="float" name="mz_value" value="10.0" min="0.0" label="m/z Value" help="m/z value for the EIC"/>
+        <param type="integer" value="10" name="tolerance_ppm" min="0" label="Tolerance (ppm)" help="Tolerance for m/z value in ppm"/>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1021/ac051437y</citation>
+            <citation type="doi">10.3390/metabo12020173</citation>
+            <citation type="doi">10.5281/zenodo.11185520</citation>
+        </citations>
+    </xml>
+</macros>
diff --git a/tools/xcms/test-data/eic_plot.png b/tools/xcms/test-data/eic_plot.png
diff --git a/tools/xcms/test-data/raw_plot.png b/tools/xcms/test-data/raw_plot.png
diff --git a/tools/xcms/test-data/xcms_plot_eic_testdata.mzML b/tools/xcms/test-data/xcms_plot_eic_testdata.mzML
diff --git a/tools/xcms/test-data/xcms_plot_raw_testdata.mzML b/tools/xcms/test-data/xcms_plot_raw_testdata.mzML
@@ -0,0 +1,212 @@
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