Mercurial > repos > iuc > compleasm

changeset 6:fc7334661489 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 9c5d5e6f1813e5c0fd496a828a1fb5e3120f188c
author iuc
date Thu, 25 Sep 2025 11:37:58 +0000
parents 7109a27a11db
children
files compleasm.xml macros.xml
diffstat 2 files changed, 22 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/compleasm.xml	Mon Jan 20 09:55:04 2025 +0000
+++ b/compleasm.xml	Thu Sep 25 11:37:58 2025 +0000
@@ -35,7 +35,6 @@
             <option value="busco" selected="true">BUSCO</option>
             <option value="lite">Lite</option>
         </param>
-
         <param argument="--specified_contigs" type="text" label="Specify the contigs to be evaluated" optional="true" help="e.g. chr1 chr2 chr3. If not specified, all contigs will be evaluated">
             <sanitizer invalid_char="">
                 <valid initial="string.letters,string.digits">
@@ -50,6 +49,7 @@
             <option value="full_table">full table</option>
             <option value="miniprot">miniprot</option>
             <option value="translated_protein">translated proteins</option>
+            <option value="summary">summary</option>
         </param>
 
         <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false">
@@ -74,6 +74,9 @@
         <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta">
             <filter>outputs and 'translated_protein' in outputs</filter>
         </data>
+        <data name='summary' format='txt' label="${tool.name} on ${on_string}: Summary" from_work_dir="galaxy_output/summary.txt">
+            <filter>outputs and 'summary' in outputs</filter>
+        </data>
     </outputs>
 
     <tests>
@@ -116,6 +119,23 @@
                 <has_text text="S:1.20%, 4"/>
             </assert_stdout>
         </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="small_genome.fasta"/>
+            <param name="mode" value="lite"/>
+            <param name="outputs" value="summary"/>
+            <param name="busco_database" value="entomoplasmatales_odb10"/>
+            <param name="lineage_dataset" value="entomoplasmatales_odb10"/>
+            <output name="summary">
+                <assert_contents>
+                    <has_text text="## lineage: entomoplasmatales_odb10"/>
+                    <has_text text="M:96.08%, 319"/>
+                    <has_text text="N:332"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="S:3.01%, 10"/>
+            </assert_stdout>
+        </test>
     </tests>
     <help><![CDATA[
 
--- a/macros.xml	Mon Jan 20 09:55:04 2025 +0000
+++ b/macros.xml	Thu Sep 25 11:37:58 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.2.6</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
 
     <xml name="citation">
         <citations>