diff Sbml2Tab.xml @ 0:897bc123f6c5 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/Sbml2Tab.xml	Thu Mar 13 15:49:53 2025 +0000
@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="@TOOL_VERSION@">
+  <description>Create a tabulated file listing reaction attributes 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 fr.inrae.toulouse.metexplore.met4j_toolbox.convert.Sbml2Tab#if str($i):
+ -irr "$i"
+#end if
+#if str($r):
+ -rev "$r"
+#end if
+ -i "$in"
+ -o "$out"
+]]></command>
+  <inputs>
+    <param argument="-irr" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text" value="--&gt;">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+    <param argument="-rev" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+    <param argument="-i" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="out"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="in" value="toy_model.xml"/>
+      <output ftype="tsv" name="out">
+        <assert_contents>
+          <has_n_lines n="8"/>
+          <has_n_columns n="9"/>
+          <has_text text="2.0 E[c] --&gt; D[c]"/>
+          <has_text text="A[c] &lt;==&gt; B[c]"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="in" value="toy_model.xml"/>
+      <param name="i" value="-&gt;"/>
+      <param name="r" value="="/>
+      <output ftype="tsv" name="out">
+        <assert_contents>
+          <has_n_lines n="8"/>
+          <has_n_columns n="9"/>
+          <has_text text="2.0 E[c] -&gt; D[c]"/>
+          <has_text text="A[c] = B[c]"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file
+@ATTRIBUTION@]]></help>
+  <citations/>
+</tool>