diff rbdock.xml @ 2:6fe6b0e10ed6 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1"

--- a/rbdock.xml	Sat Apr 25 08:58:20 2020 -0400
+++ b/rbdock.xml	Wed Jun 03 12:56:21 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="rxdock_rbdock" name="rxDock docking" version="0.1.4" profile="19.01">
+<tool id="rxdock_rbdock" name="rxDock docking" version="0.1.5" profile="19.01">
     <description>- perform protein-ligand docking with rxDock</description>
     <macros>
         <import>rxdock_macros.xml</import>
@@ -22,8 +22,11 @@
   ln -s '$ligands' ligands.sdf &&
 #end if
 
-python '$__tool_directory__/rbdock.py'
+rbdock -i ligands.sdf
+    -r receptor.prm
+    -p dock.prm
     -n '$num'
+    -o rdock_output
     #if $seed:
         -s '$seed'
     #end if
@@ -98,7 +101,7 @@
     </outputs>
     <tests>
         <!-- broken ligand test -->
-        <test expect_failure="true" expect_exit_code="23">
+        <test>
             <param name="receptor" value="receptor.mol2"/>
             <param name="ligands" value="broken_ligand.sdf"/>
             <param name="active_site" value="receptor.as"/>
@@ -110,6 +113,13 @@
                 <param name="top" value="1"/>
             </conditional>
             <param name="name" value="false"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Rbt.Current_Directory"/>
+                    <has_n_lines n="181"/>
+                    <has_text_matching expression="^([^\$]+?\$\$\$\$){1}?$"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="receptor" value="receptor.mol2"/>
@@ -126,7 +136,8 @@
             <output name="output">
                 <assert_contents>
                     <has_text text="Rbt.Current_Directory"/>
-                    <has_n_lines n="355"/>
+                    <has_n_lines n="352"/>
+                    <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/>
                 </assert_contents>
             </output>
         </test>
@@ -145,7 +156,8 @@
             <output name="output">
                 <assert_contents>
                     <has_text text="Rbt.Current_Directory"/>
-                     <has_n_lines n="355"/>
+                     <has_n_lines n="352"/>
+                    <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/>
                 </assert_contents>
             </output>
         </test>
@@ -164,7 +176,8 @@
             <output name="output">
                 <assert_contents>
                     <has_text text="Rbt.Current_Directory"/>
-                    <has_n_lines n="1059"/>
+                    <has_n_lines n="1056"/>
+                    <has_text_matching expression="^([^\$]+?\$\$\$\$){6}?$"/>
                 </assert_contents>
             </output>
         </test>
@@ -185,6 +198,7 @@
                 <assert_contents>
                     <has_text text="Rbt.Current_Directory"/>
                      <has_n_lines n="355"/>
+                    <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/>
                 </assert_contents>
             </output>
         </test>
@@ -207,6 +221,7 @@
                 <assert_contents>
                     <has_text text="Rbt.Current_Directory"/>
                      <has_n_lines n="355"/>
+                    <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/>
                 </assert_contents>
             </output>
         </test>