Mercurial > repos > metexplore > met4j_formulamapper

changeset 0:c9f248f68f60 draft

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 538e93b3d7804d3e2d6a8d83aea3853279d37de3-dirty
author metexplore
date Tue, 28 Oct 2025 15:01:20 +0000
parents
children 927af2eb6534
files FormulaMapper.xml macros.xml
diffstat 2 files changed, 47 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FormulaMapper.xml	Tue Oct 28 15:01:20 2025 +0000
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_FormulaMapper" name="FormulaMapper" version="@TOOL_VERSION@">
+  <description>Map a list of formulas against metabolites from a SBML file</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="bio_tools"/>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[met4j mapping.FormulaMapper -i "$sbmlPath"
+ -f "$inputPath"
+ $na
+ -o "$outputPath"
+]]></command>
+  <inputs>
+    <param argument="-i" format="sbml" label="input SBML file" name="sbmlPath" optional="false" type="data" value=""/>
+    <param argument="-f" format="tsv" label="input formula file (one per line)" name="inputPath" optional="false" type="data" value=""/>
+    <param argument="-na" checked="false" falsevalue="" label="Output formulas without match in model, with NA value" name="na" truevalue="-na" type="boolean" value="false"/>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="outputPath"/>
+  </outputs>
+  <tests/>
+  <help><![CDATA[
+@ATTRIBUTION@]]></help>
+  <citations/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 28 15:01:20 2025 +0000
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<!-- This file has been automatically generated by the met4j app GenerateGalaxyFiles. Please don't edit manually. -->
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.2.0">met4j</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">met4j</xref>
+        </xrefs>
+    </xml>
+    <token name="@TOOL_VERSION@">2.2.0</token>
+    <token name="@ATTRIBUTION@"><![CDATA[
+**Attribution**
+
+This Galaxy tool relies on the met4j toolkit which is dedicated to the structural analysis of metabolic networks (https://forgemia.inra.fr/metexplore/met4j)
+    ]]></token>
+</macros>
\ No newline at end of file