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diff ete_lineage_generator.xml @ 11:2db72467da51 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 67e136d433c0d925db362342919305b46fdffecd"
author earlhaminst
date Thu, 10 Mar 2022 14:01:44 +0000
parents f1eca1158f21
children d40b9a7debe5
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--- a/ete_lineage_generator.xml	Fri Nov 20 16:56:22 2020 +0000
+++ b/ete_lineage_generator.xml	Thu Mar 10 14:01:44 2022 +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="@VERSION@+galaxy1">
     <description>from a list of species/taxids using the ETE Toolkit</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -120,6 +120,19 @@
             <param name="includeid" value="--includeid" />
             <output name="outputFile" file="lineage-wid.txt" />
         </test>
+        <test>
+            <param name="speciesFile" ftype="txt" value="species_ids.txt" />
+            <param name="database" ftype="sqlite" value="taxdump.sqlite" />
+            <output name="outputFile">
+                <assert_contents>
+                    <has_line line="9606&#009;Eukaryota&#009;Chordata&#009;Mammalia&#009;Euarchontoglires&#009;Hominoidea&#009;Homo&#009;Homo sapiens"/>
+                    <has_line line="0&#009;NA&#009;NA&#009;NA&#009;NA&#009;NA&#009;NA&#009;NA"/>
+                </assert_contents>
+            </output>
+            <assert_stderr>
+                <has_line line="[0] could not determine lineage!"/>
+            </assert_stderr>
+        </test>
     </tests>
     <help><![CDATA[
 Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_.