# HG changeset patch
# User bgruening
# Date 1518427354 18000
# Node ID 5327811c2835581c425a62eee9b2422d4538745a
# Parent  f0ddfdc80f8e89f7b865392770aae9b59abb655c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787

diff -r f0ddfdc80f8e -r 5327811c2835 docking.xml
--- a/docking.xml	Sat Jun 04 08:56:08 2016 -0400
+++ b/docking.xml	Mon Feb 12 04:22:34 2018 -0500
@@ -28,142 +28,142 @@
         </test>
     </tests>
     <help><![CDATA[
-        ** What it does? **
+**What it does?**
 
-        This tool performs molecular docking with Autodock Vina program.
+This tool performs molecular docking with Autodock Vina program.
 
-        ** inputs **
+**Inputs**
 
-        Three inputs are required for use this tools. The first is a text file with the box configurations, this file looks like the following example:
+Three inputs are required for use this tools. The first is a text file with the box configurations, this file looks like the following example::
 
-        size_x =  20.00
-        size_y =  18.40
-        size_z =  23.60
-        center_x =  70.92
-        center_y =  70.57
-        center_z =  36.86
-        num_modes = 9999
-        energy_range = 9999
-        exhaustiveness = 10
-        cpu = 4
-        seed = 1
+    size_x =  20.00
+    size_y =  18.40
+    size_z =  23.60
+    center_x =  70.92
+    center_y =  70.57
+    center_z =  36.86
+    num_modes = 9999
+    energy_range = 9999
+    exhaustiveness = 10
+    cpu = 4
+    seed = 1
 
-        Where the parameters size_x, size_y, size_z, center_x, center_y and center_z  are coordinates of the binding site. 
-        The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm.
+Where the parameters size_x, size_y, size_z, center_x, center_y and center_z  are coordinates of the binding site. 
+The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm.
 
-        The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool.
-        The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool.
+The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool.
+The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool.
 
-        ** outputs **
+**Outputs**
 
-        Two outputs are generated by this tool. The first is a pdbqt file with the molecule structure resulting of the molecular docking, this file looks like the following example:
+Two outputs are generated by this tool. The first is a pdbqt file with the molecule structure resulting of the molecular docking, this file looks like the following example::
 
-        MODEL 1
-        REMARK VINA RESULT:      -0.0      0.000      0.000
-        REMARK  9 active torsions:
-        REMARK  status: ('A' for Active; 'I' for Inactive)
-        REMARK    1  A    between atoms: C_2  and  O_3 
-        REMARK    2  A    between atoms: C_2  and  C_14 
-        REMARK    3  A    between atoms: O_3  and  C_4 
-        REMARK    4  A    between atoms: C_4  and  C_5 
-        REMARK    5  A    between atoms: C_6  and  C_8 
-        REMARK    6  A    between atoms: C_8  and  C_9 
-        REMARK    7  A    between atoms: C_9  and  C_10 
-        REMARK    8  A    between atoms: C_16  and  O_17 
-        REMARK    9  A    between atoms: C_19  and  O_20 
-        ROOT
-        ATOM      1  O   LIG d   1      72.801  71.157  37.352  0.00  0.00    -0.259 OA
-        ATOM      2  C   LIG d   1      73.413  72.112  37.794  0.00  0.00     0.293 C 
-        ENDROOT
-        BRANCH   2   3
-        ATOM      3  O   LIG d   1      72.912  73.321  38.144  0.00  0.00    -0.314 OA
-        BRANCH   3   4
-        ATOM      4  C   LIG d   1      71.868  73.332  39.120  0.00  0.00     0.206 C 
-        BRANCH   4   5
-        ATOM      5  C   LIG d   1      72.522  73.555  40.453  0.00  0.00     0.002 C 
-        ATOM      6  C   LIG d   1      72.762  72.629  41.405  0.00  0.00    -0.085 C 
-        ATOM      7  C   LIG d   1      72.390  71.176  41.274  0.00  0.00     0.043 C 
-        BRANCH   6   8
-        ATOM      8  C   LIG d   1      73.435  73.012  42.714  0.00  0.00     0.037 C 
-        BRANCH   8   9
-        ATOM      9  C   LIG d   1      74.184  74.348  42.631  0.00  0.00     0.031 C 
-        BRANCH   9  10
-        ATOM     10  C   LIG d   1      75.668  74.175  42.431  0.00  0.00    -0.024 C 
-        ATOM     11  C   LIG d   1      76.399  74.547  41.360  0.00  0.00    -0.091 C 
-        ATOM     12  C   LIG d   1      75.833  75.151  40.104  0.00  0.00     0.042 C 
-        ATOM     13  C   LIG d   1      77.897  74.373  41.339  0.00  0.00     0.042 C 
-        ENDBRANCH   9  10
-        ENDBRANCH   8   9
-        ENDBRANCH   6   8
-        ENDBRANCH   4   5
-        ENDBRANCH   3   4
-        ENDBRANCH   2   3
-        BRANCH   2  14
-        ATOM     14  C   LIG d   1      74.882  72.132  38.012  0.00  0.00     0.042 A 
-        ATOM     15  C   LIG d   1      75.732  72.845  37.153  0.00  0.00     0.057 A 
-        ATOM     16  C   LIG d   1      77.101  72.826  37.385  0.00  0.00     0.099 A 
-        ATOM     17  C   LIG d   1      77.623  72.116  38.462  0.00  0.00     0.098 A 
-        ATOM     18  C   LIG d   1      76.791  71.422  39.330  0.00  0.00     0.040 A 
-        ATOM     19  C   LIG d   1      75.412  71.432  39.110  0.00  0.00     0.020 A 
-        BRANCH  16  20
-        ATOM     20  O   LIG d   1      77.978  73.498  36.578  0.00  0.00    -0.358 OA
-        ATOM     21  HO  LIG d   1      77.680  74.093  35.900  1.00  0.00     0.217 HD
-        ENDBRANCH  16  20
-        BRANCH  17  22
-        ATOM     22  O   LIG d   1      78.971  72.100  38.675  0.00  0.00    -0.358 OA
-        ATOM     23  HO  LIG d   1      79.541  71.651  38.060  1.00  0.00     0.217 HD
-        ENDBRANCH  17  22
-        ENDBRANCH   2  14
-        TORSDOF 9
-        ENDMDL 
+    MODEL 1
+    REMARK VINA RESULT:      -0.0      0.000      0.000
+    REMARK  9 active torsions:
+    REMARK  status: ('A' for Active; 'I' for Inactive)
+    REMARK    1  A    between atoms: C_2  and  O_3 
+    REMARK    2  A    between atoms: C_2  and  C_14 
+    REMARK    3  A    between atoms: O_3  and  C_4 
+    REMARK    4  A    between atoms: C_4  and  C_5 
+    REMARK    5  A    between atoms: C_6  and  C_8 
+    REMARK    6  A    between atoms: C_8  and  C_9 
+    REMARK    7  A    between atoms: C_9  and  C_10 
+    REMARK    8  A    between atoms: C_16  and  O_17 
+    REMARK    9  A    between atoms: C_19  and  O_20 
+    ROOT
+    ATOM      1  O   LIG d   1      72.801  71.157  37.352  0.00  0.00    -0.259 OA
+    ATOM      2  C   LIG d   1      73.413  72.112  37.794  0.00  0.00     0.293 C 
+    ENDROOT
+    BRANCH   2   3
+    ATOM      3  O   LIG d   1      72.912  73.321  38.144  0.00  0.00    -0.314 OA
+    BRANCH   3   4
+    ATOM      4  C   LIG d   1      71.868  73.332  39.120  0.00  0.00     0.206 C 
+    BRANCH   4   5
+    ATOM      5  C   LIG d   1      72.522  73.555  40.453  0.00  0.00     0.002 C 
+    ATOM      6  C   LIG d   1      72.762  72.629  41.405  0.00  0.00    -0.085 C 
+    ATOM      7  C   LIG d   1      72.390  71.176  41.274  0.00  0.00     0.043 C 
+    BRANCH   6   8
+    ATOM      8  C   LIG d   1      73.435  73.012  42.714  0.00  0.00     0.037 C 
+    BRANCH   8   9
+    ATOM      9  C   LIG d   1      74.184  74.348  42.631  0.00  0.00     0.031 C 
+    BRANCH   9  10
+    ATOM     10  C   LIG d   1      75.668  74.175  42.431  0.00  0.00    -0.024 C 
+    ATOM     11  C   LIG d   1      76.399  74.547  41.360  0.00  0.00    -0.091 C 
+    ATOM     12  C   LIG d   1      75.833  75.151  40.104  0.00  0.00     0.042 C 
+    ATOM     13  C   LIG d   1      77.897  74.373  41.339  0.00  0.00     0.042 C 
+    ENDBRANCH   9  10
+    ENDBRANCH   8   9
+    ENDBRANCH   6   8
+    ENDBRANCH   4   5
+    ENDBRANCH   3   4
+    ENDBRANCH   2   3
+    BRANCH   2  14
+    ATOM     14  C   LIG d   1      74.882  72.132  38.012  0.00  0.00     0.042 A 
+    ATOM     15  C   LIG d   1      75.732  72.845  37.153  0.00  0.00     0.057 A 
+    ATOM     16  C   LIG d   1      77.101  72.826  37.385  0.00  0.00     0.099 A 
+    ATOM     17  C   LIG d   1      77.623  72.116  38.462  0.00  0.00     0.098 A 
+    ATOM     18  C   LIG d   1      76.791  71.422  39.330  0.00  0.00     0.040 A 
+    ATOM     19  C   LIG d   1      75.412  71.432  39.110  0.00  0.00     0.020 A 
+    BRANCH  16  20
+    ATOM     20  O   LIG d   1      77.978  73.498  36.578  0.00  0.00    -0.358 OA
+    ATOM     21  HO  LIG d   1      77.680  74.093  35.900  1.00  0.00     0.217 HD
+    ENDBRANCH  16  20
+    BRANCH  17  22
+    ATOM     22  O   LIG d   1      78.971  72.100  38.675  0.00  0.00    -0.358 OA
+    ATOM     23  HO  LIG d   1      79.541  71.651  38.060  1.00  0.00     0.217 HD
+    ENDBRANCH  17  22
+    ENDBRANCH   2  14
+    TORSDOF 9
+    ENDMDL 
 
-        The last is a log file with the binding affinity scores, this file looks like the following example:
+The last is a log file with the binding affinity scores, this file looks like the following example::
 
-        -----------------------------------------------------------------
-         If you used AutoDock Vina in your work, please cite:          
-                                                                       
-         O. Trott, A. J. Olson,                                        
-         AutoDock Vina: improving the speed and accuracy of docking    
-         with a new scoring function, efficient optimization and       
-         multithreading, Journal of Computational Chemistry 31 (2010)  
-         455-461                                                       
-                                                                       
-         DOI 10.1002/jcc.21334                                         
-                                                                       
-         Please see http://vina.scripps.edu for more information.      
-        ------------------------------------------------------------------
+    -----------------------------------------------------------------
+     If you used AutoDock Vina in your work, please cite:          
+                                                                   
+     O. Trott, A. J. Olson,                                        
+     AutoDock Vina: improving the speed and accuracy of docking    
+     with a new scoring function, efficient optimization and       
+     multithreading, Journal of Computational Chemistry 31 (2010)  
+     455-461                                                       
+                                                                   
+     DOI 10.1002/jcc.21334                                         
+                                                                   
+     Please see http://vina.scripps.edu for more information.      
+    ------------------------------------------------------------------
 
-        Reading input ... done.
-        Setting up the scoring function ... done.
-        Analyzing the binding site ... done.
-        Using random seed: 1899908181
-        Performing search ... done.
-        Refining results ... done.
+    Reading input ... done.
+    Setting up the scoring function ... done.
+    Analyzing the binding site ... done.
+    Using random seed: 1899908181
+    Performing search ... done.
+    Refining results ... done.
 
-        mode |   affinity | dist from best mode
-             | (kcal/mol) | rmsd l.b.| rmsd u.b.
-        -----+------------+----------+----------
-           1         -0.0      0.000      0.000
-           2         -0.0      2.046      2.443
-           3         -0.0      5.896      7.949
-           4         -0.0      2.518      3.100
-           5         -0.0      2.417      4.527
-           6         -0.0      5.686      7.689
-           7         -0.0      2.828      4.792
-           8         -0.0      5.547      7.086
-           9         -0.0      7.388      9.966
-          10         -0.0      7.877     11.352
-          11         -0.0      8.203     10.157
-          12         -0.0      5.163      7.653
-          13         -0.0      3.093      6.011
-          14         -0.0      7.998     11.146
-          15         -0.0      7.015     10.108
-          16         -0.0      8.795     11.682
-          17         -0.0      7.317     10.367
-          18          0.0      3.274      4.160
-          19          0.0     10.286     12.001
-          20          0.0      3.566      5.349
-        Writing output ... done.
+    mode |   affinity | dist from best mode
+         | (kcal/mol) | rmsd l.b.| rmsd u.b.
+    -----+------------+----------+----------
+       1         -0.0      0.000      0.000
+       2         -0.0      2.046      2.443
+       3         -0.0      5.896      7.949
+       4         -0.0      2.518      3.100
+       5         -0.0      2.417      4.527
+       6         -0.0      5.686      7.689
+       7         -0.0      2.828      4.792
+       8         -0.0      5.547      7.086
+       9         -0.0      7.388      9.966
+      10         -0.0      7.877     11.352
+      11         -0.0      8.203     10.157
+      12         -0.0      5.163      7.653
+      13         -0.0      3.093      6.011
+      14         -0.0      7.998     11.146
+      15         -0.0      7.015     10.108
+      16         -0.0      8.795     11.682
+      17         -0.0      7.317     10.367
+      18          0.0      3.274      4.160
+      19          0.0     10.286     12.001
+      20          0.0      3.566      5.349
+    Writing output ... done.
     ]]></help>
     <citations>
         <citation type="doi">10.1002/jcc.21334</citation>