diff GetBiggModelProteome.xml @ 0:f1505c753689 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/GetBiggModelProteome.xml	Thu Mar 13 15:46:36 2025 +0000
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="@TOOL_VERSION@">
+  <description>Get proteome in fasta format of a model present in the BIGG database</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.bigg.GetBiggModelProteome -m "$modelId"
+ -o "$outputFile"
+]]></command>
+  <inputs>
+    <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="outputFile"/>
+  </outputs>
+  <tests>
+    <test maxseconds="120">
+      <param name="modelId" value="e_coli_core"/>
+      <output ftype="fasta" name="outputFile">
+        <assert_contents>
+          <has_line_matching expression=".*name=.*" n="136"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database
+@ATTRIBUTION@]]></help>
+  <citations>
+    <citation type="doi">10.1093/nar/gkv1049</citation>
+  </citations>
+</tool>