Mercurial > repos > earlhaminst > ete

diff ete_lineage_generator.xml @ 16:e4d5d9a69c9d draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit a0d7ab86b86bb764e457767bf8e8bc29868d0cbb
author earlhaminst
date Mon, 10 Mar 2025 23:28:17 +0000
parents 1e85af7a29c4
children
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line diff
--- a/ete_lineage_generator.xml	Mon Feb 24 16:34:12 2025 +0000
+++ b/ete_lineage_generator.xml	Mon Mar 10 23:28:17 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ete_lineage_generator" name="ETE lineage generator" version="@VERSION@">
+<tool id="ete_lineage_generator" name="ETE lineage generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>from a list of species/taxids using the ETE Toolkit</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -88,37 +88,53 @@
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="compress" value="" />
-            <param name="levels" value="full" />
+            <conditional name="compresscond">
+                <param name="compress" value="" />
+            </conditional>
+            <conditional name="ranks">
+                <param name="levels" value="full" />
+            </conditional>
             <output name="outputFile" file="lineage.txt" />
         </test>
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="compress" value="-c" />
-            <param name="levels" value="primary" />
+            <conditional name="compresscond">
+                <param name="compress" value="-c" />
+            </conditional>
+            <conditional name="ranks">
+                <param name="levels" value="primary" />
+            </conditional>
             <output name="outputFile" file="lineage-compress.txt" />
         </test>
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="compress" value="-c" />
-            <param name="levels" value="primary" />
-            <param name="lower" value="-l" />
+            <conditional name="compresscond">
+                <param name="compress" value="-c" />
+                <param name="lower" value="true" />
+            </conditional>
+            <conditional name="ranks">
+                <param name="levels" value="primary" />
+            </conditional>
             <output name="outputFile" file="lineage-compress-lower.txt" />
         </test>
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="compress" value="" />
-            <param name="levels" value="manual" />
-            <param name="manualranks" value="kingdom,family" />
+            <conditional name="compresscond">
+                <param name="compress" value="" />
+            </conditional>
+            <conditional name="ranks">
+                <param name="levels" value="manual" />
+                <param name="manualranks" value="kingdom,family" />
+            </conditional>
             <output name="outputFile" file="lineage-full.txt" />
         </test>
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="includeid" value="--includeid" />
+            <param name="includeid" value="true" />
             <output name="outputFile" file="lineage-wid.txt" />
         </test>
         <test>