Compleasm: use symlink instead of copying busco data

Author: abretaud

tools/compleasm/compleasm.xml

@@ -11,17 +11,17 @@
     </requirements>
     <version_command>compleasm --version</version_command>
     <command><![CDATA[
-    
-    mkdir -p galaxy_db &&
-    cp -r '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/' &&
+    mkdir -p 'galaxy_db/' &&
+    ln -s '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/${lineage_dataset}' &&
+    touch 'galaxy_db/${lineage_dataset}.done' &&
 
     compleasm run
     -a '$input'
     -o galaxy_output
     --mode $mode
     -L 'galaxy_db'
     -l '$lineage_dataset'
-    -t "\${GALAXY_SLOTS:-1}" 
+    -t "\${GALAXY_SLOTS:-1}"
 
     #if str($specified_contigs) != '':
         --specified_contigs '$specified_contigs'
@@ -43,7 +43,7 @@
             </sanitizer>
             <validator type="regex">[0-9a-zA-Z_ ]+</validator>
         </param>
-        
+
         <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
             <option value="full_table_busco" selected="true">full busco table</option>
             <option value="full_table">full table</option>
@@ -72,26 +72,32 @@
         </data>
         <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>
     </outputs>
 
     <tests>
         <test expect_num_outputs="4">
             <param name="input" value="small_genome.fasta"/>
             <param name="mode" value="busco"/>
             <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/>
-            <param name="busco_database" value="eukaryota_odb10"/>
-            <param name="lineage_dataset" value="eukaryota_odb10"/>
+            <param name="busco_database" value="entomoplasmatales_odb10"/>
+            <param name="lineage_dataset" value="entomoplasmatales_odb10"/>
             <output name="full_table_busco">
                 <assert_contents>
                     <has_text text="Busco id"/>
-                    <has_text text="Missing"/>
+                    <has_text text="496at186328&#009;Missing"/>
+                    <has_text text="165at186328&#009;Complete"/>
+                    <has_text text="421at186328&#009;Complete"/>
+                    <has_text text="90at186328&#009;Complete"/>
                 </assert_contents>
             </output>
             <output name="full_table">
                 <assert_contents>
-                    <has_text text="Gene"/>
-                    <has_text text="Missing"/>
+                    <has_text text="Gene&#009;Status"/>
+                    <has_text text="496at186328&#009;Missing"/>
+                    <has_text text="165at186328&#009;Single"/>
+                    <has_text text="421at186328&#009;Single"/>
+                    <has_text text="90at186328&#009;Single"/>
                 </assert_contents>
             </output>
             <output name="miniprot">
@@ -101,19 +107,22 @@
             </output>
             <output name="translated_protein">
                 <assert_contents>
-                    <has_text text="GGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGG"/>
-                    <has_text text="AAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAHVTLQQLDLCSLDSVRAAADALRTAYPRIDVLINNAGVMW"/>
+                    <has_text text="EKDFYQELGVSSDASPEEIKRAYRKLARDLHPDANPGNPAA"/>
+                    <has_text text="AASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVD"/>
                 </assert_contents>
             </output>
+            <assert_stdout>
+                <has_text text="S:1.20%, 4"/>
+            </assert_stdout>
         </test>
     </tests>
     <help><![CDATA[
 
-    compleasm_ assesses genome completeness based on genome assembly. 
+    compleasm_ assesses genome completeness based on genome assembly.
 
     .. _compleasm: https://github.com/huangnengCSU/compleasm
 
-    ]]>    
+    ]]>
     </help>
     <expand macro="citation"/>
 </tool>

tools/compleasm/macros.xml

@@ -1,10 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">0.2.6</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
 
     <xml name="citation">
         <citations>
-            <citation type="doi">10.1101/2023.06.03.543588</citation> 
+            <citation type="doi">10.1101/2023.06.03.543588</citation>
         </citations>
     </xml>
 

tools/compleasm/test-data/busco_database.loc

@@ -2,5 +2,5 @@
 # - value
 # - name
 # - version
-# - /path/to/data 
-eukaryota_odb10	eukaryota	5.4.6	${__HERE__}/test-db/busco_downloads
+# - /path/to/data
+entomoplasmatales_odb10	entomoplasmatales	5.4.6	${__HERE__}/test-db/busco_downloads