diff ExtractAnnotations.xml @ 0:ff7c095b236d 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/ExtractAnnotations.xml	Thu Mar 13 15:42:00 2025 +0000
@@ -0,0 +1,75 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="@TOOL_VERSION@">
+  <description>Extract databases' references from SBML annotations or notes.</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.ExtractAnnotations -i "$inputPath"
+ -export "$export"
+ -db "$db"
+ $uniq
+ $skip
+ -o "$outputPath"
+]]></command>
+  <inputs>
+    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
+    <param argument="-export" label="the type of entity to extract annotation, either metabolite, reaction, or gene" name="export" optional="false" type="select" value="METABOLITE">
+      <option selected="true" value="METABOLITE">METABOLITE</option>
+      <option value="REACTION">REACTION</option>
+      <option value="GENE">GENE</option>
+    </param>
+    <param argument="-db" label="name of the referenced database to export annotations from, as listed in notes or identifiers.org base uri" name="db" optional="false" type="text" value="">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+    <param argument="-uniq" checked="false" falsevalue="" label="keep only one identifier if multiple are referenced for the same entity" name="uniq" truevalue="-uniq" type="boolean" value="false"/>
+    <param argument="-skip" checked="false" falsevalue="" label="Skip entities without the selected annotations, by default output them with NA value" name="skip" truevalue="-skip" type="boolean" value="false"/>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="outputPath"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="inputPath" value="Human-GEM_pathways.xml"/>
+      <param name="export" value="METABOLITE"/>
+      <param name="db" value="metanetx.chemical"/>
+      <output ftype="tsv" name="outputPath">
+        <assert_contents>
+          <has_n_lines n="146"/>
+          <has_n_columns n="2"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="inputPath" value="Human-GEM_pathways.xml"/>
+      <param name="export" value="METABOLITE"/>
+      <param name="db" value="metanetx.chemical"/>
+      <param name="skip" value="true"/>
+      <output ftype="tsv" name="outputPath">
+        <assert_contents>
+          <has_n_lines n="145"/>
+          <has_n_columns n="2"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="inputPath" value="Human-GEM_pathways.xml"/>
+      <param name="export" value="METABOLITE"/>
+      <param name="db" value="metanetx.chemical"/>
+      <param name="skip" value="true"/>
+      <param name="uniq" value="true"/>
+      <output ftype="tsv" name="outputPath">
+        <assert_contents>
+          <has_n_lines n="111"/>
+          <has_n_columns n="2"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri.
+@ATTRIBUTION@]]></help>
+  <citations/>
+</tool>