Update biobb_train_mdae.xml

galaxycomputationalchemistry · Jul 8, 2024 · 021d2ea · 021d2ea
1 parent 2b562df
commit 021d2ea
Showing 1 changed file with 9 additions and 8 deletions.
diff --git a/tools/biobb_pytorch/biobb_train_mdae.xml b/tools/biobb_pytorch/biobb_train_mdae.xml
@@ -1,20 +1,21 @@
 <tool id="biobb_pytorch_train_mdae" name="TrainMdae" version="@TOOL_VERSION@" profile="22.05">
-    <description>Train a Molecular Dynamics AutoEncoder (MDAE) PyTorch model</description>
+    <description>Train a Molecular Dynamics AutoEncoder (MDAE) PyTorch model.</description>
     <macros>
       <token name="@TOOL_VERSION@">4.2.1</token>
     </macros>
 
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">biobb_pytorch</requirement>
     </requirements>
+
     <command detect_errors="exit_code"><![CDATA[
 
-      ln -s $input_train_npy_path ./input_train_npy_path.$input_train_npy_path.ext;
+      ln -s '$input_train_npy_path' ./input_train_npy_path.$input_train_npy_path.ext &&
       #if $input_model_pth_path:
-        ln -s $input_model_pth_path ./input_model_pth_path.$input_model_pth_path.ext;
+        ln -s '$input_model_pth_path' ./input_model_pth_path.$input_model_pth_path.ext &&
       #end if
       #if $config_json:
-        ln -s $config_json ./config_json.$config_json.ext;
+        ln -s '$config_json' ./config_json.$config_json.ext &&
       #end if
 
       train_mdae
@@ -36,9 +37,9 @@
       #end if
       ;
 
-      mv $outname_output_model_pth_path $output_model_pth_path;
-      if test -f $outname_output_train_data_npz_path; then mv $outname_output_train_data_npz_path $output_train_data_npz_path; fi;
-      if test -f $outname_output_performance_npz_path; then mv $outname_output_performance_npz_path $output_performance_npz_path; fi;
+      mv '$outname_output_model_pth_path' '$output_model_pth_path' &&
+      if test -f '$outname_output_train_data_npz_path'; then mv '$outname_output_train_data_npz_path' '$output_train_data_npz_path'; fi;
+      if test -f '$outname_output_performance_npz_path'; then mv '$outname_output_performance_npz_path' '$output_performance_npz_path'; fi;
 
       ]]>
     </command>
@@ -110,4 +111,4 @@ Check the syntax for the tool parameters at the original library documentation:
         </citation>
         <citation type="doi">10.1038/s41597-019-0177-4</citation>
     </citations>
-</tool>
+</tool>