diff ExtractPathways.xml @ 0:effdd70905ed draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ExtractPathways.xml	Thu Mar 13 15:42:11 2025 +0000
@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_ExtractPathways" name="ExtractPathways" version="@TOOL_VERSION@">
+  <description>Extract pathway(s) from a SBML file and create a sub-network SBML file</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="bio_tools"/>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[met4j fr.inrae.toulouse.metexplore.met4j_toolbox.attributes.ExtractPathways -i "$inputPath"
+ -p "$pathwayId"
+ -o "$outputPath"
+]]></command>
+  <inputs>
+    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
+    <param argument="-p" label="pathway identifiers, separated by &quot;+&quot; sign if more than one" name="pathwayId" optional="false" type="text" value="">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="sbml" name="outputPath"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="inputPath" value="XF_network.sbml"/>
+      <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/>
+      <output ftype="sbml" name="outputPath">
+        <assert_contents>
+          <is_valid_xml/>
+          <has_line_matching expression=".*&lt;reaction.*" n="17"/>
+          <has_line_matching expression=".*groups:id=.*" n="2"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file
+@ATTRIBUTION@]]></help>
+  <citations/>
+</tool>