XCMS tools for plotting EIC and Peaks

tools/xcms/.shed.yml

@@ -0,0 +1,17 @@
+name: xcms_plot
+owner: recetox
+remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/plot_eic"
+homepage_url: "https://github.com/RECETOX/galaxytools"
+categories:
+  - Metabolomics
+description: XCMS and Spectra plotting tools
+long_description: |
+
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "{{ tool_name }} tool from the xcms package"
+suite:
+  name: suite_xcms_plot
+  description: tools from xcms are used for visualization of raw data
+  type: repository_suite_definition

tools/xcms/macros.xml

@@ -0,0 +1,21 @@
+<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>
+</macros>

tools/xcms/test-data/xcms_plot_raw_testdata.mzML

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tools/xcms/xcms_plot_eic.xml

@@ -0,0 +1,51 @@
+<tool id="xcms_plot_eic" name="Plot Extracted Ion Chromatogram" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+    <description>Plot the extracted ion chromatogram (EIC) from mzML file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript -e 'source("${plot_eic}")'
+    ]]></command>
+    <configfiles>
+        <configfile name="plot_eic">
+library(xcms)
+library(MsExperiment)
+library(Spectra)
+mse = readMsExperiment(file.path('${input}'))
+offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
+chr = chromatogram(mse, mz = ${mz_value} + c(-offset, offset), msLevel = ${mslevel})
+png(filename = '${output_filename}')
+plot(chr)
+dev.off()
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param type="data" name="input" format="mzML" label="Input mzML file"/>
+        <param type="float" name="mz_value" value="0" label="m/z Value" help="m/z value for the EIC"/>
+        <param type="integer" value="10" name="tolerance_ppm" label="Tolerance (ppm)" help="Tolerance for m/z value in ppm"/>
+        <param type="integer" value="1" name="mslevel" label="MS Level" help="MS level for the EIC"/>
+    </inputs>
+    <outputs>
+        <data name="output_filename" format="png" label="EIC plot at m/z=$mz_value of $input.element_identifier"  />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="xcms_plot_eic_testdata.mzML"/>
+            <param name="mz_value" value="153.06614"/>
+            <param name="tolerance_ppm" value="10"/>
+            <param name="mslevel" value="1"/>
+            <output name="output_filename" file="eic_plot.png"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool plots the extracted ion chromatogram (EIC) from an mzML file, using a provided m/z value. 
+        It uses a default tolerance of 10 ppm and operates at mslevel 1 by default.    
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/ac051437y</citation>
+    </citations>
+</tool>