# HG changeset patch
# User bgruening
# Date 1557250335 14400
# Node ID f6eb53a200df144d2511afb9b29c9039c07c1114
# Parent  1b4a6ebd9898d89a91e473dce2a67a25baa531c9
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e

diff -r 1b4a6ebd9898 -r f6eb53a200df prepare_ligand.xml
--- a/prepare_ligand.xml	Mon Feb 12 04:23:29 2018 -0500
+++ b/prepare_ligand.xml	Tue May 07 13:32:15 2019 -0400
@@ -1,5 +1,5 @@
 <tool id="prepare_ligand" name="Prepare ligand" version="0.1.0">
-    <description>Tool to prepare ligand for Autodock Vina</description>
+    <description>for docking with Autodock Vina</description>
     <requirements>
         <requirement type="package" version="1.5.6">mgltools</requirement>
     </requirements>
@@ -22,125 +22,138 @@
         </test>
     </tests>
     <help><![CDATA[
-**What it does?**
+
+.. class:: infomark
+
+**What this tool does**
 
-This tool uses the MGLTools programming packages to convert a mol2 molecule file to pdbqt molecule file, what is the Autodock Vina program uses to perform molecular docking.
+This tool uses the MGLTools programming package to convert a mol2 molecule file to a pdbqt molecule file, which the Autodock Vina program uses to perform molecular docking. The output file has a similar format to the pdb input, with atom types modified to conform to AutoDock atom types and an extra column containing Gasteiger charges added.
+
+-----
+
+.. class:: infomark
 
 **Input**
 
-It's required at least one mol2 dataset in history, what is informed in ligand field, for use the tool. The mol2 molecule file looks like the following example::
+A mol2 file is required to use this tool.
 
-    @<TRIPOS>MOLECULE
-    NuBBE_1
-     21 21 0 0 0
-    SMALL
-    GASTEIGER
+* Example::
 
-    @<TRIPOS>ATOM
-          1 O          -0.9469   -0.4359   -3.2099 O.2     1  LIG1       -0.2449
-          2 C          -1.2069    0.2449   -2.2351 C.2     1  LIG1        0.3396
-          3 O          -1.9353   -0.1138   -1.1515 O.3     1  LIG1       -0.4570
-          4 C          -2.3385   -1.4828   -1.0650 C.3     1  LIG1        0.1113
-          5 C          -1.7447   -2.0319    0.2001 C.2     1  LIG1       -0.0480
-          6 C          -0.5501   -2.6439    0.3381 C.2     1  LIG1       -0.0731
-          7 C           0.4046   -2.8855   -0.8015 C.3     1  LIG1       -0.0437
-          8 C          -0.0862   -3.1529    1.6937 C.3     1  LIG1       -0.0285
-          9 C           0.7304   -2.1137    2.4728 C.3     1  LIG1       -0.0308
-         10 C           1.1870   -2.6184    3.8183 C.2     1  LIG1       -0.0850
-         11 C           2.3521   -3.2333    4.1099 C.2     1  LIG1       -0.0796
-         12 C           3.4007   -3.6048    3.0986 C.3     1  LIG1       -0.0440
-         13 C           2.6989   -3.6136    5.5272 C.3     1  LIG1       -0.0440
-         14 C          -0.7776    1.6572   -2.0661 C.ar    1  LIG1        0.0627
-         15 C          -0.6402    2.2240   -0.7903 C.ar    1  LIG1       -0.0026
-         16 C          -0.2486    3.5509   -0.6768 C.ar    1  LIG1        0.1590
-         17 O          -0.1045    4.1587    0.5397 O.3     1  LIG1       -0.5033
-         18 C           0.0124    4.3080   -1.8161 C.ar    1  LIG1        0.1583
-         19 O           0.3891    5.6141   -1.6913 O.3     1  LIG1       -0.5033
-         20 C          -0.1020    3.7535   -3.0825 C.ar    1  LIG1       -0.0158
-         21 C          -0.4936    2.4191   -3.2122 C.ar    1  LIG1       -0.0441
-    @<TRIPOS>BOND
-         1     1     2    2
-         2     2     3    1
-         3     3     4    1
-         4     4     5    1
-         5     5     6    2
-         6     6     7    1
-         7     6     8    1
-         8     8     9    1
-         9     9    10    1
-        10    10    11    2
-        11    11    12    1
-        12    11    13    1
-        13     2    14    1
-        14    14    15   ar
-        15    15    16   ar
-        16    16    17    1
-        17    16    18   ar
-        18    18    19    1
-        19    18    20   ar
-        20    20    21   ar
-        21    14    21   ar
+        @<TRIPOS>MOLECULE
+        NuBBE_1
+        21 21 0 0 0
+        SMALL
+        GASTEIGER
+        @<TRIPOS>ATOM
+            1 O          -0.9469   -0.4359   -3.2099 O.2     1  LIG1       -0.2449
+            2 C          -1.2069    0.2449   -2.2351 C.2     1  LIG1        0.3396
+            3 O          -1.9353   -0.1138   -1.1515 O.3     1  LIG1       -0.4570
+            4 C          -2.3385   -1.4828   -1.0650 C.3     1  LIG1        0.1113
+            5 C          -1.7447   -2.0319    0.2001 C.2     1  LIG1       -0.0480
+            6 C          -0.5501   -2.6439    0.3381 C.2     1  LIG1       -0.0731
+            7 C           0.4046   -2.8855   -0.8015 C.3     1  LIG1       -0.0437
+            8 C          -0.0862   -3.1529    1.6937 C.3     1  LIG1       -0.0285
+            9 C           0.7304   -2.1137    2.4728 C.3     1  LIG1       -0.0308
+            10 C           1.1870   -2.6184    3.8183 C.2     1  LIG1       -0.0850
+            11 C           2.3521   -3.2333    4.1099 C.2     1  LIG1       -0.0796
+            12 C           3.4007   -3.6048    3.0986 C.3     1  LIG1       -0.0440
+            13 C           2.6989   -3.6136    5.5272 C.3     1  LIG1       -0.0440
+            14 C          -0.7776    1.6572   -2.0661 C.ar    1  LIG1        0.0627
+            15 C          -0.6402    2.2240   -0.7903 C.ar    1  LIG1       -0.0026
+            16 C          -0.2486    3.5509   -0.6768 C.ar    1  LIG1        0.1590
+            17 O          -0.1045    4.1587    0.5397 O.3     1  LIG1       -0.5033
+            18 C           0.0124    4.3080   -1.8161 C.ar    1  LIG1        0.1583
+            19 O           0.3891    5.6141   -1.6913 O.3     1  LIG1       -0.5033
+            20 C          -0.1020    3.7535   -3.0825 C.ar    1  LIG1       -0.0158
+            21 C          -0.4936    2.4191   -3.2122 C.ar    1  LIG1       -0.0441
+        @<TRIPOS>BOND
+            1     1     2    2
+            2     2     3    1
+            3     3     4    1
+            4     4     5    1
+            5     5     6    2
+            6     6     7    1
+            7     6     8    1
+            8     8     9    1
+            9     9    10    1
+            10    10    11    2
+            11    11    12    1
+            12    11    13    1
+            13     2    14    1
+            14    14    15   ar
+            15    15    16   ar
+            16    16    17    1
+            17    16    18   ar
+            18    18    19    1
+            19    18    20   ar
+            20    20    21   ar
+            21    14    21   ar
+
+-----
+
+.. class:: infomark
 
 **Output**
 
-The output is a pdbqt molecule file converted from a mol2 molecule file. The pdbqt molecule file looks like the following example::
+The output is a pdbqt molecule file.
+
+* Example::
 
-    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      -0.947  -0.436  -3.210  0.00  0.00    -0.259 OA
-    ATOM      2  C   LIG d   1      -1.207   0.245  -2.235  0.00  0.00     0.293 C 
-    ENDROOT
-    BRANCH   2   3
-    ATOM      3  O   LIG d   1      -1.935  -0.114  -1.151  0.00  0.00    -0.314 OA
-    BRANCH   3   4
-    ATOM      4  C   LIG d   1      -2.338  -1.483  -1.065  0.00  0.00     0.206 C 
-    BRANCH   4   5
-    ATOM      5  C   LIG d   1      -1.745  -2.032   0.200  0.00  0.00     0.002 C 
-    ATOM      6  C   LIG d   1      -0.550  -2.644   0.338  0.00  0.00    -0.085 C 
-    ATOM      7  C   LIG d   1       0.405  -2.885  -0.801  0.00  0.00     0.043 C 
-    BRANCH   6   8
-    ATOM      8  C   LIG d   1      -0.086  -3.153   1.694  0.00  0.00     0.037 C 
-    BRANCH   8   9
-    ATOM      9  C   LIG d   1       0.730  -2.114   2.473  0.00  0.00     0.031 C 
-    BRANCH   9  10
-    ATOM     10  C   LIG d   1       1.187  -2.618   3.818  0.00  0.00    -0.024 C 
-    ATOM     11  C   LIG d   1       2.352  -3.233   4.110  0.00  0.00    -0.091 C 
-    ATOM     12  C   LIG d   1       3.401  -3.605   3.099  0.00  0.00     0.042 C 
-    ATOM     13  C   LIG d   1       2.699  -3.614   5.527  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      -0.778   1.657  -2.066  0.00  0.00     0.042 A 
-    ATOM     15  C   LIG d   1      -0.640   2.224  -0.790  0.00  0.00     0.057 A 
-    ATOM     16  C   LIG d   1      -0.249   3.551  -0.677  0.00  0.00     0.099 A 
-    ATOM     17  C   LIG d   1       0.012   4.308  -1.816  0.00  0.00     0.098 A 
-    ATOM     18  C   LIG d   1      -0.102   3.753  -3.083  0.00  0.00     0.040 A 
-    ATOM     19  C   LIG d   1      -0.494   2.419  -3.212  0.00  0.00     0.020 A 
-    BRANCH  16  20
-    ATOM     20  O   LIG d   1      -0.104   4.159   0.540  0.00  0.00    -0.358 OA
-    ATOM     21  HO  LIG d   1       0.164   5.067   0.617  1.00  0.00     0.217 HD
-    ENDBRANCH  16  20
-    BRANCH  17  22
-    ATOM     22  O   LIG d   1       0.389   5.614  -1.691  0.00  0.00    -0.358 OA
-    ATOM     23  HO  LIG d   1       0.567   6.131  -2.469  1.00  0.00     0.217 HD
-    ENDBRANCH  17  22
-    ENDBRANCH   2  14
-    TORSDOF 9
-
+        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      -0.947  -0.436  -3.210  0.00  0.00    -0.259 OA
+        ATOM      2  C   LIG d   1      -1.207   0.245  -2.235  0.00  0.00     0.293 C 
+        ENDROOT
+        BRANCH   2   3
+        ATOM      3  O   LIG d   1      -1.935  -0.114  -1.151  0.00  0.00    -0.314 OA
+        BRANCH   3   4
+        ATOM      4  C   LIG d   1      -2.338  -1.483  -1.065  0.00  0.00     0.206 C 
+        BRANCH   4   5
+        ATOM      5  C   LIG d   1      -1.745  -2.032   0.200  0.00  0.00     0.002 C 
+        ATOM      6  C   LIG d   1      -0.550  -2.644   0.338  0.00  0.00    -0.085 C 
+        ATOM      7  C   LIG d   1       0.405  -2.885  -0.801  0.00  0.00     0.043 C 
+        BRANCH   6   8
+        ATOM      8  C   LIG d   1      -0.086  -3.153   1.694  0.00  0.00     0.037 C 
+        BRANCH   8   9
+        ATOM      9  C   LIG d   1       0.730  -2.114   2.473  0.00  0.00     0.031 C 
+        BRANCH   9  10
+        ATOM     10  C   LIG d   1       1.187  -2.618   3.818  0.00  0.00    -0.024 C 
+        ATOM     11  C   LIG d   1       2.352  -3.233   4.110  0.00  0.00    -0.091 C 
+        ATOM     12  C   LIG d   1       3.401  -3.605   3.099  0.00  0.00     0.042 C 
+        ATOM     13  C   LIG d   1       2.699  -3.614   5.527  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      -0.778   1.657  -2.066  0.00  0.00     0.042 A 
+        ATOM     15  C   LIG d   1      -0.640   2.224  -0.790  0.00  0.00     0.057 A 
+        ATOM     16  C   LIG d   1      -0.249   3.551  -0.677  0.00  0.00     0.099 A 
+        ATOM     17  C   LIG d   1       0.012   4.308  -1.816  0.00  0.00     0.098 A 
+        ATOM     18  C   LIG d   1      -0.102   3.753  -3.083  0.00  0.00     0.040 A 
+        ATOM     19  C   LIG d   1      -0.494   2.419  -3.212  0.00  0.00     0.020 A 
+        BRANCH  16  20
+        ATOM     20  O   LIG d   1      -0.104   4.159   0.540  0.00  0.00    -0.358 OA
+        ATOM     21  HO  LIG d   1       0.164   5.067   0.617  1.00  0.00     0.217 HD
+        ENDBRANCH  16  20
+        BRANCH  17  22
+        ATOM     22  O   LIG d   1       0.389   5.614  -1.691  0.00  0.00    -0.358 OA
+        ATOM     23  HO  LIG d   1       0.567   6.131  -2.469  1.00  0.00     0.217 HD
+        ENDBRANCH  17  22
+        ENDBRANCH   2  14
+        TORSDOF 9
     ]]></help>
     <citations>
         <citation type="doi">10.1002/jcc.21334</citation>