# HG changeset patch
# User bgruening
# Date 1591203381 14400
# Node ID 6fe6b0e10ed64c2f96e5a79226959b49fea1db1d
# Parent  07309bad01df7dc00d494b412d9504bd476b4249
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1"

diff -r 07309bad01df -r 6fe6b0e10ed6 rbdock.py
--- a/rbdock.py	Sat Apr 25 08:58:20 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-import subprocess
-import argparse
-
-def main():
-    parser = argparse.ArgumentParser(description='Simple wrapper for rbdock')
-    parser.add_argument('-n', '--num', type=int, help='Number of docking poses to generate')
-    parser.add_argument('-s', '--seed', type=int, help='Random seed')
-    args = parser.parse_args()
-
-    cmd = ['rbdock', '-i', 'ligands.sdf', '-r', 'receptor.prm', '-p', 'dock.prm', '-n', str(args.num), '-o', 'rdock_output']
-    if args.seed != None:
-        cmd += ['-s', str(args.seed)]
-
-    ps = subprocess.Popen(cmd, stdout=subprocess.PIPE)
-
-    error_counter = 0
-    for stdout_line in iter(ps.stdout.readline, ''):
-        if 'RBT_DOCKING_ERROR' in str(stdout_line):
-                error_counter += 1
-                if error_counter == 10:
-                    print(ps.stdout)
-                    exit(23)
-        if ps.poll() != None:
-            print(ps.stdout)
-            exit(int(ps.poll()))
-
-if __name__ == "__main__":
-    main()
diff -r 07309bad01df -r 6fe6b0e10ed6 rbdock.xml
--- 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>
diff -r 07309bad01df -r 6fe6b0e10ed6 rxdock_macros.xml
--- a/rxdock_macros.xml	Sat Apr 25 08:58:20 2020 -0400
+++ b/rxdock_macros.xml	Wed Jun 03 12:56:21 2020 -0400
@@ -6,7 +6,7 @@
     </xml>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2013.1.0_b93747f3">rxdock</requirement>
+            <requirement type="package" version="2013.1.1_148c5bd1">rxdock</requirement>
         </requirements>
     </xml>
 </macros>