diff MassMapper.xml @ 0:4928b239a36d draft

planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 71335d4a636672d264cc4f443c07856907571928

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MassMapper.xml	Fri Nov 21 10:21:26 2025 +0000
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_MassMapper" name="MassMapper" version="@TOOL_VERSION@">
+  <description>Retrieve metabolites in a SBML file from their mass.</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="bio_tools"/>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[met4j mapping.MassMapper -i "$sbmlPath"
+ -m "$inputPath"
+#if str($ppm) != 'nan':
+ -ppm "$ppm"
+#end if
+ $na
+#if str($compute):
+ -comp "$compute"
+#end if
+ -o "$outputPath"
+]]></command>
+  <inputs>
+    <param argument="-i" format="sbml" label="input SBML file" name="sbmlPath" optional="false" type="data" value=""/>
+    <param argument="-m" format="tsv" label="input mass file (one per line)" name="inputPath" optional="false" type="data" value=""/>
+    <param argument="-ppm" label="mass delta tolerance in part per million" name="ppm" optional="true" type="float" value="5.0"/>
+    <param argument="-na" checked="false" falsevalue="" label="Output mass without match in model, with NA value" name="na" truevalue="-na" type="boolean" value="false"/>
+    <param argument="-comp" label="Method for computing mass from formulas" name="compute" optional="true" type="select" value="average">
+      <option selected="true" value="average">average</option>
+      <option value="monoisotopic">monoisotopic</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="outputPath"/>
+  </outputs>
+  <tests/>
+  <help><![CDATA[Retrieve metabolites in a SBML file from their mass.
+The SBML file is expected to contain fbc:chemicalFormula attributes for species entries, in order to compute masses.
+The input mass file should contain one mass per line. The output is a tab delimited file with two columns: query mass, sbml metabolite id (one line per match)
+@ATTRIBUTION@]]></help>
+  <citations/>
+</tool>