Mercurial > repos > workflow4metabolomics > xcms_plot_eic

changeset 1:cbedca3ba6e1 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
author workflow4metabolomics
date Thu, 15 May 2025 17:02:59 +0000 (11 hours ago)
parents 51015f22fcb7
children
files macros_xcms_plot.xml xcms_plot_eic.xml
diffstat 2 files changed, 7 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/macros_xcms_plot.xml	Mon Jul 15 16:03:37 2024 +0000
+++ b/macros_xcms_plot.xml	Thu May 15 17:02:59 2025 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">4.0.0</token>
+    <token name="@TOOL_VERSION@">4.4.0</token>
     <xml name="creator">
         <creator>
             <person
@@ -24,9 +24,10 @@
         </xrefs>
     </xml>
     <xml name="base_params">
-        <param type="data" name="input" format="mzML" label="Input mzML file"/>
+        <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"/>
+        <param type="integer" value="10" name="tolerance_ppm" min="0" label="Tolerance (ppm)" help="Tolerance for m/z value in ppm. Tolerance is applied on both sides (+-)."/>
+        <param type="integer" value="1" name="mslevel" min="1" label="MS Level" help="MS level for the EIC"/>
     </xml>
     <xml name="citations">
         <citations>
--- a/xcms_plot_eic.xml	Mon Jul 15 16:03:37 2024 +0000
+++ b/xcms_plot_eic.xml	Thu May 15 17:02:59 2025 +0000
@@ -16,6 +16,9 @@
 library(xcms)
 library(MsExperiment)
 library(Spectra)
+
+sessionInfo()
+
 mse = readMsExperiment(file.path('${input}'))
 offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
 chr = chromatogram(mse, mz = ${mz_value} + c(-offset, offset), msLevel = ${mslevel})
@@ -26,7 +29,6 @@
     </configfiles>
     <inputs>
         <expand macro="base_params"/>
-        <param type="integer" value="1" name="mslevel" min="1" label="MS Level" help="MS level for the EIC"/>
     </inputs>
     <outputs>
         <data name="output_filename" format="png" label="EIC plot at m/z=$mz_value of $input.element_identifier"  />