# HG changeset patch
# User chemteam
# Date 1560412349 14400
# Node ID a1a204464657424c80481198d1d9c3716ac36f33

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc

diff -r 000000000000 -r a1a204464657 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 13 03:52:29 2019 -0400
@@ -0,0 +1,20 @@
+<macros>
+  <token name="@VERSION@">19.0</token>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="19.0">ambertools</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <xml name="citations">
+    <citations>
+      <citation type="doi">10.1002/jcc.20290</citation>
+      <citation type="bibtex">
+        @misc{ambertools, author = {D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A.
+        Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo,
+        J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman }, year = {2018}, title = {AMBER 2018}, publisher = {University of California, San Francisco}, url =
+        {http://ambermd.org/CiteAmber.php}, }</citation>
+      <yield/>
+    </citations>
+  </xml>
+</macros>
diff -r 000000000000 -r a1a204464657 parmchk2.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parmchk2.xml	Thu Jun 13 03:52:29 2019 -0400
@@ -0,0 +1,81 @@
+<tool id="ambertools_parmchk2" name="ParmChk2" version="@VERSION@">
+  <description>Amber's parameter checker</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <command detect_errors="exit_code">
+    <![CDATA[
+    parmchk2 -i '$input1'
+        -f '$input1.ext'
+        -s '$allparams.s'
+        -a '$allparams.a'
+        -o '$output1'
+        ]]>
+  </command>
+  <inputs>
+    <param type="data" name="input1" label="Molecular input (mol2)" format="mol2"/>
+    <section name="allparams" title="General Parameters" expanded="true">
+      <param name="s" type="select" display="radio" label="FFparm set parameter" help="(-s)">
+        <option selected="True" value="1">1: gaff</option>
+        <option value="2">2: gaff2</option>
+      </param>
+      <param name="a" type="boolean" checked="false" truevalue="Y" falsevalue="N" label="Print all force field parameters" help="(-a)"/>
+    </section>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output1" label="${tool.name}: frcmod output"></data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="LigA_prmchk.mol2"/>
+      <section name="allparams">
+        <param name="s" value="2"/>
+      </section>
+      <output name="output1" file="LigA_output.txt" compare="diff" lines_diff="0"></output>
+    </test>
+  </tests>
+  <help>
+    <![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Antechamber parameter check reads in a mol2 file and writes out a force field modification (frcmod) file containing any force field parameters that are needed for the molecule but not supplied by the force field file.
+Problematic parameters, if any, are indicated in the frcmod file with the note, “ATTN, need revision”, and are typically given values of zero.
+
+
+.. class:: infomark
+
+**How it works**
+
+- Select a mol input file (mol2)
+- Choose GAFF or GAFF2 parameter set
+
+.. class:: infomark
+
+**Outputs created**
+
+- Outputs a frcmod file as text
+
+.. class:: infomark
+
+**User guide and documentation**
+
+- AmberTools `userguide`_
+
+
+.. _`userguide`: http://ambermd.org/doc12/Amber19.pdf
+
+.. class:: infomark
+
+**Feature requests**
+
+Go to Galaxy Computational Chemistry and make a `feature request`_
+
+.. _`feature request`: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/new
+
+]]>
+  </help>
+  <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r a1a204464657 test-data/LigA.mol2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA.mol2	Thu Jun 13 03:52:29 2019 -0400
@@ -0,0 +1,61 @@
+@<TRIPOS>MOLECULE
+LigA
+24 24 1 0 0 
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+  1 C       49.2110    26.9920    85.5530 C.2   1 <1>  -0.3000 
+  2 H       49.1050    28.0330    85.7020 H     1 <1>   0.1500 
+  3 H       48.8320    26.6060    84.6410 H     1 <1>   0.1500 
+  4 C       49.8460    26.1960    86.4430 C.2   1 <1>  -0.1733 
+  5 C       50.0590    24.7460    86.2630 C.2   1 <1>   1.0500 
+  6 O       50.4810    24.0440    87.2160 O.co2 1 <1>  -0.9000 
+  7 O       49.8330    24.2110    85.1490 O.co2 1 <1>  -0.9000 
+  8 O       50.3730    26.8140    87.5890 O.3   1 <1>  -0.3567 
+  9 C       51.7280    27.3660    87.5930 C.3   1 <1>   0.3382 
+ 10 H       51.8840    27.9250    88.5040 H     1 <1>   0.0800 
+ 11 C       51.8170    28.2920    86.3980 C.2   1 <1>  -0.2882 
+ 12 H       51.3990    29.2560    86.5300 H     1 <1>   0.1500 
+ 13 C       52.1840    27.8630    85.1670 C.2   1 <1>  -0.2500 
+ 14 C       52.8190    26.5610    85.0450 C.2   1 <1>  -0.1500 
+ 15 H       53.0370    26.2220    84.0630 H     1 <1>   0.1500 
+ 16 C       53.1170    25.8090    86.1190 C.2   1 <1>  -0.2882 
+ 17 H       53.5700    24.8590    86.0130 H     1 <1>   0.1500 
+ 18 C       52.7610    26.1980    87.5410 C.3   1 <1>   0.3382 
+ 19 H       52.3530    25.3480    88.0710 H     1 <1>   0.0800 
+ 20 O       54.0020    26.6280    88.1730 O.3   1 <1>  -0.6800 
+ 21 H       54.4570    27.1880    87.5220 H     1 <1>   0.4000 
+ 22 C       51.9410    28.6780    83.9640 C.2   1 <1>   1.0500 
+ 23 O       51.9100    29.9280    84.0860 O.co2 1 <1>  -0.9000 
+ 24 O       51.8570    28.1570    82.8230 O.co2 1 <1>  -0.9000 
+@<TRIPOS>BOND
+  1   1   2  1   
+  2   1   3  1   
+  3   1   4  2   
+  4   4   5  1   
+  5   4   8  1   
+  6   5   6  ar  
+  7   5   7  ar  
+  8   8   9  1   
+  9   9  10  1   
+ 10   9  11  1   
+ 11   9  18  1   
+ 12  11  12  1   
+ 13  11  13  2   
+ 14  13  14  1   
+ 15  13  22  1   
+ 16  14  15  1   
+ 17  14  16  2   
+ 18  16  17  1   
+ 19  16  18  1   
+ 20  18  19  1   
+ 21  18  20  1   
+ 22  20  21  1   
+ 23  22  23  ar  
+ 24  22  24  ar  
+@<TRIPOS>SUBSTRUCTURE
+  1 ****  13 GROUP 4 **** **** 0
+
+# MOE 2016.08 (io_trps.svl 2016.04)
diff -r 000000000000 -r a1a204464657 test-data/LigA.pdb
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA.pdb	Thu Jun 13 03:52:29 2019 -0400
@@ -0,0 +1,26 @@
+CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
+ATOM      1  C   <1> X   1      49.211  26.992  85.553  0.00  0.00            
+ATOM      2  H   <1> X   1      49.105  28.033  85.702  0.00  0.00            
+ATOM      3  H   <1> X   1      48.832  26.606  84.641  0.00  0.00            
+ATOM      4  C   <1> X   1      49.846  26.196  86.443  0.00  0.00            
+ATOM      5  C   <1> X   1      50.059  24.746  86.263  0.00  0.00            
+ATOM      6  O   <1> X   1      50.481  24.044  87.216  0.00  0.00            
+ATOM      7  O   <1> X   1      49.833  24.211  85.149  0.00  0.00            
+ATOM      8  O   <1> X   1      50.373  26.814  87.589  0.00  0.00            
+ATOM      9  C   <1> X   1      51.728  27.366  87.593  0.00  0.00            
+ATOM     10  H   <1> X   1      51.884  27.925  88.504  0.00  0.00            
+ATOM     11  C   <1> X   1      51.817  28.292  86.398  0.00  0.00            
+ATOM     12  H   <1> X   1      51.399  29.256  86.530  0.00  0.00            
+ATOM     13  C   <1> X   1      52.184  27.863  85.167  0.00  0.00            
+ATOM     14  C   <1> X   1      52.819  26.561  85.045  0.00  0.00            
+ATOM     15  H   <1> X   1      53.037  26.222  84.063  0.00  0.00            
+ATOM     16  C   <1> X   1      53.117  25.809  86.119  0.00  0.00            
+ATOM     17  H   <1> X   1      53.570  24.859  86.013  0.00  0.00            
+ATOM     18  C   <1> X   1      52.761  26.198  87.541  0.00  0.00            
+ATOM     19  H   <1> X   1      52.353  25.348  88.071  0.00  0.00            
+ATOM     20  O   <1> X   1      54.002  26.628  88.173  0.00  0.00            
+ATOM     21  H   <1> X   1      54.457  27.188  87.522  0.00  0.00            
+ATOM     22  C   <1> X   1      51.941  28.678  83.964  0.00  0.00            
+ATOM     23  O   <1> X   1      51.910  29.928  84.086  0.00  0.00            
+ATOM     24  O   <1> X   1      51.857  28.157  82.823  0.00  0.00            
+END
diff -r 000000000000 -r a1a204464657 test-data/LigA_output.mol2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_output.mol2	Thu Jun 13 03:52:29 2019 -0400
@@ -0,0 +1,59 @@
+@<TRIPOS>MOLECULE
+MOL
+   24    24     1     0     0
+SMALL
+bcc
+
+
+@<TRIPOS>ATOM
+      1 C           49.2110    26.9920    85.5530 c2         1 MOL      -0.311000
+      2 H           49.1050    28.0330    85.7020 ha         1 MOL       0.109500
+      3 H1          48.8320    26.6060    84.6410 ha         1 MOL       0.109500
+      4 C1          49.8460    26.1960    86.4430 ce         1 MOL       0.022900
+      5 C2          50.0590    24.7460    86.2630 ce         1 MOL       0.384200
+      6 O           50.4810    24.0440    87.2160 o          1 MOL      -0.575500
+      7 O1          49.8330    24.2110    85.1490 o          1 MOL      -0.575500
+      8 O2          50.3730    26.8140    87.5890 os         1 MOL      -0.351900
+      9 C3          51.7280    27.3660    87.5930 c3         1 MOL       0.157300
+     10 H2          51.8840    27.9250    88.5040 h1         1 MOL       0.051700
+     11 C4          51.8170    28.2920    86.3980 c2         1 MOL      -0.174200
+     12 H3          51.3990    29.2560    86.5300 ha         1 MOL       0.141000
+     13 C5          52.1840    27.8630    85.1670 ce         1 MOL      -0.149200
+     14 C6          52.8190    26.5610    85.0450 ce         1 MOL      -0.081000
+     15 H4          53.0370    26.2220    84.0630 ha         1 MOL       0.142000
+     16 C7          53.1170    25.8090    86.1190 c2         1 MOL      -0.248200
+     17 H5          53.5700    24.8590    86.0130 ha         1 MOL       0.104000
+     18 C8          52.7610    26.1980    87.5410 c3         1 MOL       0.131300
+     19 H6          52.3530    25.3480    88.0710 h1         1 MOL       0.151700
+     20 O3          54.0020    26.6280    88.1730 oh         1 MOL      -0.611800
+     21 H7          54.4570    27.1880    87.5220 ho         1 MOL       0.374000
+     22 C9          51.9410    28.6780    83.9640 ce         1 MOL       0.376200
+     23 O4          51.9100    29.9280    84.0860 o          1 MOL      -0.587000
+     24 O5          51.8570    28.1570    82.8230 o          1 MOL      -0.587000
+@<TRIPOS>BOND
+     1     1     2 1   
+     2     1     3 1   
+     3     1     4 2   
+     4     4     5 1   
+     5     4     8 1   
+     6     5     6 2   
+     7     5     7 1   
+     8     8     9 1   
+     9     9    10 1   
+    10     9    11 1   
+    11     9    18 1   
+    12    11    12 1   
+    13    11    13 2   
+    14    13    14 1   
+    15    13    22 1   
+    16    14    15 1   
+    17    14    16 2   
+    18    16    17 1   
+    19    16    18 1   
+    20    18    19 1   
+    21    18    20 1   
+    22    20    21 1   
+    23    22    23 2   
+    24    22    24 1   
+@<TRIPOS>SUBSTRUCTURE
+     1 MOL         1 TEMP              0 ****  ****    0 ROOT
diff -r 000000000000 -r a1a204464657 test-data/LigA_output.pdb
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_output.pdb	Thu Jun 13 03:52:29 2019 -0400
@@ -0,0 +1,24 @@
+ATOM      1  C   MOL     1      49.211  26.992  85.553  1.00  0.00           C
+ATOM      2  H   MOL     1      49.105  28.033  85.702  1.00  0.00           H
+ATOM      3  H1  MOL     1      48.832  26.606  84.641  1.00  0.00           H
+ATOM      4  C1  MOL     1      49.846  26.196  86.443  1.00  0.00           C
+ATOM      5  C2  MOL     1      50.059  24.746  86.263  1.00  0.00           C
+ATOM      6  O   MOL     1      50.481  24.044  87.216  1.00  0.00           O
+ATOM      7  O1  MOL     1      49.833  24.211  85.149  1.00  0.00           O
+ATOM      8  O2  MOL     1      50.373  26.814  87.589  1.00  0.00           O
+ATOM      9  C3  MOL     1      51.728  27.366  87.593  1.00  0.00           C
+ATOM     10  H2  MOL     1      51.884  27.925  88.504  1.00  0.00           H
+ATOM     11  C4  MOL     1      51.817  28.292  86.398  1.00  0.00           C
+ATOM     12  H3  MOL     1      51.399  29.256  86.530  1.00  0.00           H
+ATOM     13  C5  MOL     1      52.184  27.863  85.167  1.00  0.00           C
+ATOM     14  C6  MOL     1      52.819  26.561  85.045  1.00  0.00           C
+ATOM     15  H4  MOL     1      53.037  26.222  84.063  1.00  0.00           H
+ATOM     16  C7  MOL     1      53.117  25.809  86.119  1.00  0.00           C
+ATOM     17  H5  MOL     1      53.570  24.859  86.013  1.00  0.00           H
+ATOM     18  C8  MOL     1      52.761  26.198  87.541  1.00  0.00           C
+ATOM     19  H6  MOL     1      52.353  25.348  88.071  1.00  0.00           H
+ATOM     20  O3  MOL     1      54.002  26.628  88.173  1.00  0.00           O
+ATOM     21  H7  MOL     1      54.457  27.188  87.522  1.00  0.00           H
+ATOM     22  C9  MOL     1      51.941  28.678  83.964  1.00  0.00           C
+ATOM     23  O4  MOL     1      51.910  29.928  84.086  1.00  0.00           O
+ATOM     24  O5  MOL     1      51.857  28.157  82.823  1.00  0.00           O
diff -r 000000000000 -r a1a204464657 test-data/LigA_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_output.txt	Thu Jun 13 03:52:29 2019 -0400
@@ -0,0 +1,21 @@
+Remark line goes here
+MASS
+
+BOND
+
+ANGLE
+
+DIHE
+
+IMPROPER
+c2-ha-c2-ha         1.1          180.0         2.0          Using the default value
+c2-c2-c2-os         1.1          180.0         2.0          Using the default value
+c2-o -c2-o          1.1          180.0         2.0          Using the default value
+c2-c3-c2-ha         1.1          180.0         2.0          Using the default value
+c2-c2-c2-c2         1.1          180.0         2.0          Using the default value
+c2-c2-c2-ha         1.1          180.0         2.0          Using the default value
+
+NONBON
+
+
+
diff -r 000000000000 -r a1a204464657 test-data/LigA_prmchk.mol2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_prmchk.mol2	Thu Jun 13 03:52:29 2019 -0400
@@ -0,0 +1,59 @@
+@<TRIPOS>MOLECULE
+MOL
+   24    24     1     0     0
+SMALL
+bcc
+
+
+@<TRIPOS>ATOM
+      1 C           49.2110    26.9920    85.5530 c2         1 MOL      -0.412000
+      2 H           49.1050    28.0330    85.7020 ha         1 MOL       0.190500
+      3 H1          48.8320    26.6060    84.6410 ha         1 MOL       0.190500
+      4 C1          49.8460    26.1960    86.4430 c2         1 MOL       0.290000
+      5 C2          50.0590    24.7460    86.2630 c2         1 MOL       0.448000
+      6 O           50.4810    24.0440    87.2160 o          1 MOL      -0.224000
+      7 O1          49.8330    24.2110    85.1490 o          1 MOL      -0.224000
+      8 O2          50.3730    26.8140    87.5890 os         1 MOL      -0.260000
+      9 C3          51.7280    27.3660    87.5930 c3         1 MOL      -0.040000
+     10 H2          51.8840    27.9250    88.5040 h1         1 MOL       0.169000
+     11 C4          51.8170    28.2920    86.3980 c2         1 MOL      -0.190000
+     12 H3          51.3990    29.2560    86.5300 ha         1 MOL       0.188000
+     13 C5          52.1840    27.8630    85.1670 c2         1 MOL       0.171000
+     14 C6          52.8190    26.5610    85.0450 c2         1 MOL      -0.190000
+     15 H4          53.0370    26.2220    84.0630 ha         1 MOL       0.188000
+     16 C7          53.1170    25.8090    86.1190 c2         1 MOL      -0.040000
+     17 H5          53.5700    24.8590    86.0130 ha         1 MOL       0.169000
+     18 C8          52.7610    26.1980    87.5410 c3         1 MOL      -0.003000
+     19 H6          52.3530    25.3480    88.0710 h1         1 MOL       0.221000
+     20 O3          54.0020    26.6280    88.1730 oh         1 MOL      -0.280000
+     21 H7          54.4570    27.1880    87.5220 ho         1 MOL       0.215000
+     22 C9          51.9410    28.6780    83.9640 c2         1 MOL       0.366000
+     23 O4          51.9100    29.9280    84.0860 o          1 MOL      -0.472500
+     24 O5          51.8570    28.1570    82.8230 o          1 MOL      -0.472500
+@<TRIPOS>BOND
+     1     1     2 1   
+     2     1     3 1   
+     3     1     4 1   
+     4     4     5 1   
+     5     4     8 1   
+     6     5     6 1   
+     7     5     7 1   
+     8     8     9 1   
+     9     9    10 1   
+    10     9    11 1   
+    11     9    18 1   
+    12    11    12 1   
+    13    11    13 1   
+    14    13    14 1   
+    15    13    22 1   
+    16    14    15 1   
+    17    14    16 1   
+    18    16    17 1   
+    19    16    18 1   
+    20    18    19 1   
+    21    18    20 1   
+    22    20    21 1   
+    23    22    23 1   
+    24    22    24 1   
+@<TRIPOS>SUBSTRUCTURE
+     1 MOL         1 TEMP              0 ****  ****    0 ROOT