changeset 0:828670ca9292 draft default tip

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IdMapper.xml	Fri Nov 21 10:21:05 2025 +0000
@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_IdMapper" name="IdMapper" version="@TOOL_VERSION@">
+  <description>Map external metabolite identifiers (kegg, metanetx, pubchem CID...) to metabolite ids 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.IdMapper -i "$sbmlPath"
+ -id "$inputPath"
+ -db "$db"
+ $na
+ -o "$outputPath"
+]]></command>
+  <inputs>
+    <param argument="-i" format="sbml" label="input SBML file" name="sbmlPath" optional="false" type="data" value=""/>
+    <param argument="-id" format="tsv" label="input external id file (one per line)" name="inputPath" optional="false" type="data" value=""/>
+    <param argument="-db" label="name of the referenced database annotations to map against, as listed in identifiers.org base uri" name="db" optional="false" type="text" value="">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+    <param argument="-na" checked="false" falsevalue="" label="Output id without matching annotation in model, with NA value" name="na" truevalue="-na" type="boolean" value="false"/>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="outputPath"/>
+  </outputs>
+  <tests/>
+  <help><![CDATA[Map external metabolite identifiers (kegg, metanetx, pubchem CID...) to metabolite ids from a SBML file.
+The SBML file is expected to contain annotations in MIRIAM format for the selected database:
+i.e, <species> entries in the sbml should contain an <annotation> field where there is references to the given database.check identifiers.org for valid database names and associated base URIs.
+The input id file should contain one id per line. The output is a tab delimited file with two columns: query id, sbml metabolite id (one line per match)
+@ATTRIBUTION@]]></help>
+  <citations/>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Nov 21 10:21:05 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>
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