diff tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml @ 5:35c9abcd8934 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598

--- a/tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml	Thu Nov 17 07:57:52 2022 +0000
+++ b/tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml	Thu Jan 12 13:45:13 2023 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="1.2.0">
+<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="1.2.1">
   <description>Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath"
 #if str($inputSide) != 'None':
@@ -25,7 +25,7 @@
 ]]></command>
   <inputs>
     <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
-    <param argument="-sc" format="" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
+    <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
     <param argument="-c" label="Selected compartment(s), as model identifiers, separated by &quot;+&quot; sign if more than one" name="comp" optional="true" type="text" value="">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
@@ -40,9 +40,50 @@
     <param argument="-in" checked="false" falsevalue="" label="if an external compartment is defined, adjust degree by considering internal counterpart" name="useInternal" truevalue="-in" type="boolean" value="false"/>
   </inputs>
   <outputs>
-    <data format="" name="outputPath"/>
+    <data format="tsv" name="outputPath"/>
   </outputs>
-  <tests/>
+  <tests>
+    <test>
+      <param name="inputPath" value="XF_network.sbml"/>
+      <param name="targetsFilePath" value="SeedsAndTargets-result.tab"/>
+      <param name="source" value="true"/>
+      <output ftype="tsv" name="outputPath">
+        <assert_contents>
+          <has_n_columns n="1"/>
+          <has_n_lines n="109"/>
+          <has_line_matching expression="M_\S+_\w" n="109"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="inputPath" value="XF_network.sbml"/>
+      <param name="targetsFilePath" value="SeedsAndTargets-result.tab"/>
+      <param name="sink" value="true"/>
+      <param name="useInternal" value="true"/>
+      <param name="comp" value="e"/>
+      <output ftype="tsv" name="outputPath">
+        <assert_contents>
+          <has_n_columns n="1"/>
+          <has_n_lines n="5"/>
+          <has_line_matching expression="^M_\S+_\w" n="5"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="inputPath" value="XF_network.sbml"/>
+      <param name="targetsFilePath" value="SeedsAndTargets-result.tab"/>
+      <param name="sink" value="true"/>
+      <param name="useBorensteinAlg" value="true"/>
+      <param name="comp" value="e"/>
+      <output ftype="tsv" name="outputPath">
+        <assert_contents>
+          <has_n_columns n="1"/>
+          <has_n_lines n="26"/>
+          <has_line_matching expression="^M_\S+_\w" n="26"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
   <help><![CDATA[Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology. Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms.
 This application can use seed definition and SCC-based detection algorithm by Borenstein et al. or, alternatively, degree-based sink and source detection with compartment adjustment.
 The first method (see Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105) consider strongly connected components rather than individual nodes, thus, members of cycles can be considered as seed. A sink from an external compartment can however be connected to a non sink internal counterpart, thus highlighting what could end up in the external compartment rather than what must be exported.