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changeset 0:520448a32548 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 16:03:26 +0000
parents
children
files macros_xcms_plot.xml test-data/raw_plot.png test-data/xcms_plot_raw_testdata.mzML xcms_plot_raw.xml
diffstat 4 files changed, 305 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_xcms_plot.xml	Mon Jul 15 16:03:26 2024 +0000
@@ -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>
\ No newline at end of file
Binary file test-data/raw_plot.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xcms_plot_raw_testdata.mzML	Mon Jul 15 16:03:26 2024 +0000
@@ -0,0 +1,212 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">
+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">
+	<cvList count="5">
+		<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+		<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
+		<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>
+		<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>
+		<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
+	</cvList>
+	<fileDescription>
+		<fileContent>
+			<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+		</fileContent>
+		<sourceFileList count="1">
+			<sourceFile id="sf_ru_0" name="RCX_06_shortened.mzML" location="file:///C:/Users/473355/Downloads">
+				<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="6c9fc5a54e7e588b4940994f66c953de66f8e8c5" />
+				<cvParam cvRef="MS" accession="MS:1000584" name="mzML format" />
+				<cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />
+			</sourceFile>
+		</sourceFileList>
+	</fileDescription>
+	<sampleList count="1">
+		<sample id="sa_0" name="">
+			<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
+			<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
+			<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
+		</sample>
+	</sampleList>
+	<softwareList count="2">
+		<software id="so_in_0" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+		<software id="so_default" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+	</softwareList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="ic_0">
+			<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+			<softwareRef ref="so_in_0" />
+		</instrumentConfiguration>
+	</instrumentConfigurationList>
+	<dataProcessingList count="1">
+		<dataProcessing id="dp_sp_0">
+			<processingMethod order="0" softwareRef="so_default">
+				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />
+				<userParam name="warning" type="xsd:string" value="fictional processing method used to fulfill format requirements" />
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" defaultSourceFileRef="sf_ru_0">
+		<userParam name="mzml_id" type="xsd:string" value="MZmine mzML export"/>
+		<spectrumList count="4" defaultDataProcessingRef="dp_sp_0">
+			<spectrum id="scan=126" index="0" defaultArrayLength="31" dataProcessingRef="dp_sp_0">
+				<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="6.0450043e09"/>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.0000-1100.0000]"/>
+				<scanList count="1">
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+					<scan >
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+						<userParam name="MS:1000130" type="xsd:string" value=""/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
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+			</spectrum>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.0000-1100.0000]"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
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+						<userParam name="MS:1000130" type="xsd:string" value=""/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="1100" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
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+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+					<scan >
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+						</scanWindowList>
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+				</scanList>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.0000-1100.0000]"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
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+						<userParam name="MS:1000130" type="xsd:string" value=""/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+							</scanWindow>
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+				</scanList>
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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_plot_raw.xml	Mon Jul 15 16:03:26 2024 +0000
@@ -0,0 +1,55 @@
+<tool id="xcms_plot_raw" name="xcms plot raw" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+    <description>Plot raw data filtered by m/z range and retention time (RT) range</description>
+    <macros>
+        <import>macros_xcms_plot.xml</import>
+    </macros>
+    <expand macro="bio.tools"/>
+    <expand macro="creator"/>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript -e 'source("${plot_raw}")'
+    ]]></command>
+    <configfiles>
+        <configfile name="plot_raw">
+library(xcms)
+library(MsExperiment)
+library(Spectra)
+mse = readMsExperiment(file.path('${input}'))
+mz_offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
+rt_offset = ${rt_range} / 2
+raw = mse |>
+    filterRt(rt = ${rt} + c(-rt_offset, rt_offset)) |>
+    filterMzRange(mz = ${mz_value} + c(-mz_offset, mz_offset))
+png(filename = '${output_filename}')
+par(oma = c(0.5, 2, 0.5, 1))
+plot(raw)
+dev.off()
+        </configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="base_params"/>
+        <param type="float" name="rt" label="Retention Time" min="0.0" value="0.0" help="Retention time for the plot"/>
+        <param type="float" name="rt_range" value="5.0" min="0.0" label="Retention Time Range" help="Retention time range for the plot"/>
+    </inputs>
+    <outputs>
+        <data name="output_filename" format="png" label="PLot at m/z=$mz_value and rt=$rt of $input.element_identifier"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="xcms_plot_raw_testdata.mzML"/>
+            <param name="mz_value" value="153.06583"/>
+            <param name="tolerance_ppm" value="10"/>
+            <param name="rt" value="171.922"/>
+            <param name="rt_range" value="0.1"/>
+            <output name="output_filename" file="raw_plot.png" compare="sim_size" delta="5000"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool plots the raw data filtered by m/z range and retention time (RT) range from an mzML file. 
+        It uses a default tolerance of 10 ppm and retention time range of 5 s. 
+        More information and detailed instructions can be found in the tutorial at: https://jorainer.github.io/xcmsTutorials/articles/xcms-preprocessing.html#data-visualization
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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