diff colabfold_alphafold.xml @ 2:9d65257c56de draft default tip

planemo upload for repository https://github.com/sokrypton/ColabFold commit b01085b7137b002268e0a8e4d75a5e03326638bb

--- a/colabfold_alphafold.xml	Mon Mar 25 17:57:44 2024 +0000
+++ b/colabfold_alphafold.xml	Wed Aug 21 07:40:05 2024 +0000
@@ -43,10 +43,11 @@
     input_data
     output
     && cd output
-    && mv *.a3m output.a3m
+    && mkdir a3m_out
     && mkdir png_out
     && mkdir json_out
     && mkdir pdb_out
+    && mv ./*.a3m a3m_out
     && mv ./*.png png_out
     && mv ./*.json json_out
     && mv ./*.pdb pdb_out
@@ -117,7 +118,9 @@
             <discover_datasets format="npy" pattern="__name_and_ext__" directory="output/npy_out"/>
             <filter>output_options['save_single_representations'] or output_options['save_pair_representations']</filter>
         </collection>
-        <data name="a3m_out" format="a3m" from_work_dir="output/output.a3m" label="${tool.name} on ${on_string}: a3m file"/>
+        <collection name="a3m" type="list" format="a3m" label="${tool.name} on ${on_string}: a3m files">
+            <discover_datasets format="a3m" pattern="__name_and_ext__" directory="output/a3m_out"/>
+        </collection>
     </outputs>
     <tests>
         <test expect_failure="true" expect_exit_code="1">