diff build/tools/ExtractPathways/ExtractPathways.xml @ 6:7a6f2380fc1d draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build/tools/ExtractPathways/ExtractPathways.xml	Wed May 17 13:26:37 2023 +0000
@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_ExtractPathways" name="ExtractPathways" version="1.3.0">
+  <description>Extract pathway(s) from GSMN</description>
+  <xrefs>
+    <xref type="bio.tools">met4j</xref>
+  </xrefs>
+  <requirements>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh 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 GSMN: From a SBML file, Create a sub-network SBML file including only a selection of pathways]]></help>
+  <citations/>
+</tool>