--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml	Fri Jul 29 13:23:40 2022 +0000
@@ -0,0 +1,50 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="1.1.0">
+  <description>Get gene lists from a list of reactions and a GSMN.</description>
+  <xrefs>
+    <xref type="bio.tools">met4j</xref>
+  </xrefs>
+  <requirements>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml"
+ -r "$reactionFile"
+#if str($sep):
+ -sep "$sep"
+#end if
+ $hasHeader
+#if str($i) != 'nan':
+ -col "$i"
+#end if
+ -o "$outputFile"
+]]></command>
+  <inputs>
+    <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
+    <param argument="-r" format="tsv" label="Input Reaction file" name="reactionFile" optional="false" type="data" value=""/>
+    <param argument="-sep" label="Separator in reaction file" name="sep" optional="true" type="text" value="&#9;">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+    <param argument="-header" checked="false" falsevalue="" label="Skip reaction file header" name="hasHeader" truevalue="-header" type="boolean" value="false"/>
+    <param argument="-col" label="Column number in reaction file (first as 1)" name="i" optional="true" type="integer" value="1"/>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="outputFile"/>
+  </outputs>
+  <tests>
+    <test>
+    <param name="sbml" value="XF_network.sbml"/>
+    <param name="reactionFile" value="XF_network_R_Seed.tab"/>
+    <output ftype="tsv" name="outputFile">
+      <assert_contents>
+        <has_n_lines n="2"/>
+        <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
+        <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
+      </assert_contents>
+    </output>
+  </test>
+  </tests>
+  <help><![CDATA[Get associated gene list from a list of reactions and a GSMN. Parse GSMN GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
+  <citations/>
+</tool>