diff xcms_plot_raw.xml @ 1:8b8d360316c3 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
author workflow4metabolomics
date Thu, 15 May 2025 17:02:56 +0000 (3 weeks ago)
parents 520448a32548
children
line wrap: on
line diff
--- a/xcms_plot_raw.xml	Mon Jul 15 16:03:26 2024 +0000
+++ b/xcms_plot_raw.xml	Thu May 15 17:02:56 2025 +0000
@@ -16,10 +16,15 @@
 library(xcms)
 library(MsExperiment)
 library(Spectra)
+
+sessionInfo()
+
 mse = readMsExperiment(file.path('${input}'))
 mz_offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
-rt_offset = ${rt_range} / 2
+rt_offset = ${rt_range}
+
 raw = mse |>
+    filterMsLevel(msLevel = ${mslevel}L) |>
     filterRt(rt = ${rt} + c(-rt_offset, rt_offset)) |>
     filterMzRange(mz = ${mz_value} + c(-mz_offset, mz_offset))
 png(filename = '${output_filename}')
@@ -31,10 +36,10 @@
     <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"/>
+        <param type="float" name="rt_range" value="5.0" min="0.0" label="Retention Time Range" help="Retention time range for the plot. Range is applied on both sides of the specified RT value (+-)."/>
     </inputs>
     <outputs>
-        <data name="output_filename" format="png" label="PLot at m/z=$mz_value and rt=$rt of $input.element_identifier"/>
+        <data name="output_filename" format="png" label="Plot at m/z=$mz_value and rt=$rt of $input.element_identifier"/>
     </outputs>
     <tests>
         <test>
@@ -42,8 +47,13 @@
             <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"/>
+            <param name="rt_range" value="5"/>
+            <output name="output_filename">
+                <assert_contents>
+                    <has_image_channels channels="3"/>
+                    <has_image_center_of_mass center_of_mass="240.30, 240.51" eps="0.1"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[