# HG changeset patch
# User bgruening
# Date 1495283516 14400
# Node ID 4c4e812a67a2b560986ff2745f910d7e01272c75
# Parent  039ef13e3676b6cf3c09780cedeebbd25c4525df
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502

diff -r 039ef13e3676 -r 4c4e812a67a2 confab.tar.bz2
Binary file confab.tar.bz2 has changed
diff -r 039ef13e3676 -r 4c4e812a67a2 confab.xml
--- a/confab.xml	Sun Nov 01 10:34:34 2015 -0500
+++ b/confab.xml	Sat May 20 08:31:56 2017 -0400
@@ -1,20 +1,23 @@
-<tool id="ctb_confab" name="Conformer calculation" version="0.1">
+<tool id="ctb_confab" name="Conformer calculation" version="0.4">
     <description>for molecules (confab)</description>
-    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <requirements>
-        <requirement type="package" version="1.0.1">confab</requirement>
+        <requirement type="package" version="2.4.1">openbabel</requirement>
     </requirements>
-    <command>
+    <command detect_errors="aggressive">
 <![CDATA[
-    confab
+
+    obabel
+        '${infile}'
+        -O '${outfile}'
         -i ${infile.ext}
         -o sdf
-        -r $RMSD
-        -e $energy
-        -c $conformers
+        --confab
+        --rcutoff $RMSD
+        --ecutoff $energy
+        --conf $conformers
         $first_conformer
-        $infile
-        $outfile 2>&1
+
 ]]>
     </command>
     <inputs>
@@ -22,7 +25,8 @@
         <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
         <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
         <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
-        <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' />
+        <param name='first_conformer' type='boolean' truevalue='--original' falsevalue=''
+            label='Include the input conformation as the first conformer' />
     </inputs>
     <outputs>
         <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
@@ -32,9 +36,9 @@
             <param name="infile" value='CID_3033.sdf' ftype='sdf' />
             <param name='RMSD'  value='0.5' />
             <param name='energy' value='50.0' />
-            <param name='conformers' value='100000' />
-            <param name='first_conformer' value='-a' />
-            <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
+            <param name='conformers' value='10' />
+            <param name='first_conformer' value="True" />
+            <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="2"/>
         </test>
     </tests>
 <help>
@@ -126,17 +130,12 @@
   9  8  1  6  0  0  0
  10  9  1  1  0  0  0
 
------
-
-.. class:: infomark
-
-**Cite**
-
-Confab_
-
-.. _Confab: https://code.google.com/p/confab/
 
 
 ]]>
     </help>
+    <citations>
+        <citation type="doi">10.1186/1758-2946-3-33</citation>
+        <citation type="doi">10.1186/1758-2946-3-8</citation>
+    </citations>
 </tool>
diff -r 039ef13e3676 -r 4c4e812a67a2 repository_dependencies.xml
--- a/repository_dependencies.xml	Sun Nov 01 10:34:34 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-</repositories>
diff -r 039ef13e3676 -r 4c4e812a67a2 test-data/confab_on_CID3033.sdf
--- a/test-data/confab_on_CID3033.sdf	Sun Nov 01 10:34:34 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,270 +0,0 @@
-214.7
- OpenBabel06291213403D
-
- 30 31  0  0  0  0  0  0  0  0999 V2000
-    1.9541    1.1500   -2.5078 Cl  0  0  0  0  0  0  0  0  0  0  0  0
-    1.1377   -1.6392    2.1136 Cl  0  0  0  0  0  0  0  0  0  0  0  0
-   -3.2620   -2.9284   -1.0647 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.7906   -1.9108    0.9092 O   0  0  0  0  0  0  0  0  0  0  0  0
-    0.2679   -0.2051   -0.3990 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.0640    0.5139   -0.3769 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.7313    0.7178   -0.0192 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.4761   -0.6830   -1.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
-    1.6571   -0.2482   -0.1795 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.0382    1.4350    0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.3728    1.8429    0.7234 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.6797    2.5600    0.7506 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.3470    2.7640    1.1083 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.5353    0.3477   -1.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.1740   -0.8865    0.9534 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.8480   -1.8749   -0.3123 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.9124    0.3058   -0.8739 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.5511   -0.9285    1.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
-    4.4203   -0.3324    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.7086   -0.9792   -1.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.3614   -0.4266   -1.7676 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.0861   -1.1146   -0.6780 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -4.0812    1.2885   -0.2604 H   0  0  0  0  0  0  0  0  0  0  0  0
-    0.6569    2.0278    1.0167 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.4382    3.2769    1.0511 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.0683    3.6399    1.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
-    4.6037    0.7654   -1.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
-    3.9635   -1.4215    2.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
-    5.4925   -0.3651    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.5025   -3.7011   -0.5102 H   0  0  0  0  0  0  0  0  0  0  0  0
-  1 14  1  0  0  0  0
-  2 15  1  0  0  0  0
-  3 16  1  0  0  0  0
-  3 30  1  0  0  0  0
-  4 16  2  0  0  0  0
-  5  7  1  0  0  0  0
-  5  9  1  0  0  0  0
-  5 22  1  0  0  0  0
-  6  7  1  0  0  0  0
-  6  8  1  0  0  0  0
-  6 10  2  0  0  0  0
-  7 11  2  0  0  0  0
-  8 16  1  0  0  0  0
-  8 20  1  0  0  0  0
-  8 21  1  0  0  0  0
-  9 14  2  0  0  0  0
-  9 15  1  0  0  0  0
- 10 12  1  0  0  0  0
- 10 23  1  0  0  0  0
- 11 13  1  0  0  0  0
- 11 24  1  0  0  0  0
- 12 13  2  0  0  0  0
- 12 25  1  0  0  0  0
- 13 26  1  0  0  0  0
- 14 17  1  0  0  0  0
- 15 18  2  0  0  0  0
- 17 19  2  0  0  0  0
- 17 27  1  0  0  0  0
- 18 19  1  0  0  0  0
- 18 28  1  0  0  0  0
- 19 29  1  0  0  0  0
-M  END
->  <PUBCHEM_COMPOUND_CID>
-3033
-
->  <PUBCHEM_CONFORMER_RMSD>
-0.6
-
->  <PUBCHEM_CONFORMER_DIVERSEORDER>
-1
-20
-18
-39
-29
-42
-38
-35
-30
-25
-33
-28
-32
-36
-26
-24
-40
-11
-27
-37
-7
-41
-10
-19
-43
-8
-6
-16
-44
-23
-34
-14
-15
-31
-9
-13
-17
-21
-22
-5
-12
-2
-3
-4
-
->  <PUBCHEM_MMFF94_PARTIAL_CHARGES>
-28
-1 -0.18
-10 -0.15
-11 -0.15
-12 -0.15
-13 -0.15
-14 0.18
-15 0.18
-16 0.66
-17 -0.15
-18 -0.15
-19 -0.15
-2 -0.18
-22 0.4
-23 0.15
-24 0.15
-25 0.15
-26 0.15
-27 0.15
-28 0.15
-29 0.15
-3 -0.65
-30 0.5
-4 -0.57
-5 -0.6
-6 -0.14
-7 0.1
-8 0.2
-9 0.1
-
->  <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
-4
-
->  <PUBCHEM_PHARMACOPHORE_FEATURES>
-7
-1 3 acceptor
-1 4 acceptor
-1 5 cation
-1 5 donor
-3 3 4 16 anion
-6 6 7 10 11 12 13 rings
-6 9 14 15 17 18 19 rings
-
->  <PUBCHEM_HEAVY_ATOM_COUNT>
-19
-
->  <PUBCHEM_ATOM_DEF_STEREO_COUNT>
-0
-
->  <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
-0
-
->  <PUBCHEM_BOND_DEF_STEREO_COUNT>
-0
-
->  <PUBCHEM_BOND_UDEF_STEREO_COUNT>
-0
-
->  <PUBCHEM_ISOTOPIC_ATOM_COUNT>
-0
-
->  <PUBCHEM_COMPONENT_COUNT>
-1
-
->  <PUBCHEM_CACTVS_TAUTO_COUNT>
-1
-
->  <PUBCHEM_CONFORMER_ID>
-00000BD900000001
-
->  <PUBCHEM_MMFF94_ENERGY>
-65.6362
-
->  <PUBCHEM_FEATURE_SELFOVERLAP>
-35.578
-
->  <PUBCHEM_SHAPE_FINGERPRINT>
-10366900 7 17386020514759110480
-114674 6 16903282898360328323
-11578080 2 17913245089295617604
-11582403 64 14544541357940910356
-11640471 11 18127963303313961600
-12236239 1 18272088352834916308
-12363563 72 18042978579496277287
-12553582 1 18190740839094073615
-12596599 1 18201439237582433270
-12788726 201 18410285909464206003
-13032168 30 18201440238019390274
-13140716 1 18187086113919468457
-13538477 17 18339642338307470464
-13583140 156 17241914119188522922
-13764800 53 17895191172601517065
-13965767 371 17259888045752176376
-14115302 16 18342181093776810149
-14787075 74 17907866106787333628
-15279307 12 18198622322777022915
-15375462 189 18270674264943931347
-15669948 3 18336550511731321249
-16752209 62 18336841852664817743
-16945 1 18188484791351783177
-19433438 48 18059583550169763352
-200 152 18130792217719576158
-20645476 183 18270115859187436189
-20905425 154 17970632883131290416
-21452121 199 18046637711133085653
-21639500 275 16988270998321974524
-22112679 90 18342446063036096292
-23419403 2 17835564502519425292
-23493267 7 18115023138028600728
-23526113 38 16660924516543134566
-23557571 272 17821721762863303772
-23559900 14 17896315990920094510
-23598288 3 18411412925846384519
-23598291 2 18059009613384180254
-238 59 16343141308025475526
-4340502 62 17273677940604857177
-6049 1 17240202131864233360
-6992083 37 18058168521433072460
-7615 1 18201433675414973908
-77492 1 18272651289913926852
-81228 2 17968373550240022809
-9709674 26 17896035610527288590
-
->  <PUBCHEM_SHAPE_MULTIPOLES>
-378.03
-7.01
-2.75
-1.77
-0.78
-1.58
-0.3
-0.41
-1.94
--1.08
-1.9
--8.69
-11.04
-2.58
-
->  <PUBCHEM_SHAPE_SELFOVERLAP>
-790.335
-
->  <PUBCHEM_SHAPE_VOLUME>
-214.7
-
->  <PUBCHEM_COORDINATE_TYPE>
-2
-5
-255
-
-$$$$
diff -r 039ef13e3676 -r 4c4e812a67a2 test-data/confab_on_CID_3033.sdf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/confab_on_CID_3033.sdf	Sat May 20 08:31:56 2017 -0400
@@ -0,0 +1,270 @@
+3033
+ OpenBabel05191717063D
+
+ 30 31  0  0  0  0  0  0  0  0999 V2000
+    1.9541    1.1500   -2.5078 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+    1.1377   -1.6392    2.1136 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+   -3.2620   -2.9284   -1.0647 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.7906   -1.9108    0.9092 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2679   -0.2051   -0.3990 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.0640    0.5139   -0.3769 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7313    0.7178   -0.0192 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4761   -0.6830   -1.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.6571   -0.2482   -0.1795 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.0382    1.4350    0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3728    1.8429    0.7234 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.6797    2.5600    0.7506 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.3470    2.7640    1.1083 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.5353    0.3477   -1.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.1740   -0.8865    0.9534 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8480   -1.8749   -0.3123 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.9124    0.3058   -0.8739 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.5511   -0.9285    1.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.4203   -0.3324    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.7086   -0.9792   -1.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.3614   -0.4266   -1.7676 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0861   -1.1146   -0.6780 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.0812    1.2885   -0.2604 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6569    2.0278    1.0167 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.4382    3.2769    1.0511 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0683    3.6399    1.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
+    4.6037    0.7654   -1.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
+    3.9635   -1.4215    2.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4925   -0.3651    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.5025   -3.7011   -0.5102 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1 14  1  0  0  0  0
+  2 15  1  0  0  0  0
+  3 16  1  0  0  0  0
+  3 30  1  0  0  0  0
+  4 16  2  0  0  0  0
+  5  7  1  0  0  0  0
+  5  9  1  0  0  0  0
+  5 22  1  0  0  0  0
+  6  7  1  0  0  0  0
+  6  8  1  0  0  0  0
+  6 10  2  0  0  0  0
+  7 11  2  0  0  0  0
+  8 16  1  0  0  0  0
+  8 20  1  0  0  0  0
+  8 21  1  0  0  0  0
+  9 14  2  0  0  0  0
+  9 15  1  0  0  0  0
+ 10 12  1  0  0  0  0
+ 10 23  1  0  0  0  0
+ 11 13  1  0  0  0  0
+ 11 24  1  0  0  0  0
+ 12 13  2  0  0  0  0
+ 12 25  1  0  0  0  0
+ 13 26  1  0  0  0  0
+ 14 17  1  0  0  0  0
+ 15 18  2  0  0  0  0
+ 17 19  2  0  0  0  0
+ 17 27  1  0  0  0  0
+ 18 19  1  0  0  0  0
+ 18 28  1  0  0  0  0
+ 19 29  1  0  0  0  0
+M  END
+>  <PUBCHEM_COMPOUND_CID>
+3033
+
+>  <PUBCHEM_CONFORMER_RMSD>
+0.6
+
+>  <PUBCHEM_CONFORMER_DIVERSEORDER>
+1
+20
+18
+39
+29
+42
+38
+35
+30
+25
+33
+28
+32
+36
+26
+24
+40
+11
+27
+37
+7
+41
+10
+19
+43
+8
+6
+16
+44
+23
+34
+14
+15
+31
+9
+13
+17
+21
+22
+5
+12
+2
+3
+4
+
+>  <PUBCHEM_MMFF94_PARTIAL_CHARGES>
+28
+1 -0.18
+10 -0.15
+11 -0.15
+12 -0.15
+13 -0.15
+14 0.18
+15 0.18
+16 0.66
+17 -0.15
+18 -0.15
+19 -0.15
+2 -0.18
+22 0.4
+23 0.15
+24 0.15
+25 0.15
+26 0.15
+27 0.15
+28 0.15
+29 0.15
+3 -0.65
+30 0.5
+4 -0.57
+5 -0.6
+6 -0.14
+7 0.1
+8 0.2
+9 0.1
+
+>  <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
+4
+
+>  <PUBCHEM_PHARMACOPHORE_FEATURES>
+7
+1 3 acceptor
+1 4 acceptor
+1 5 cation
+1 5 donor
+3 3 4 16 anion
+6 6 7 10 11 12 13 rings
+6 9 14 15 17 18 19 rings
+
+>  <PUBCHEM_HEAVY_ATOM_COUNT>
+19
+
+>  <PUBCHEM_ATOM_DEF_STEREO_COUNT>
+0
+
+>  <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
+0
+
+>  <PUBCHEM_BOND_DEF_STEREO_COUNT>
+0
+
+>  <PUBCHEM_BOND_UDEF_STEREO_COUNT>
+0
+
+>  <PUBCHEM_ISOTOPIC_ATOM_COUNT>
+0
+
+>  <PUBCHEM_COMPONENT_COUNT>
+1
+
+>  <PUBCHEM_CACTVS_TAUTO_COUNT>
+1
+
+>  <PUBCHEM_CONFORMER_ID>
+00000BD900000001
+
+>  <PUBCHEM_MMFF94_ENERGY>
+65.6362
+
+>  <PUBCHEM_FEATURE_SELFOVERLAP>
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diff -r 039ef13e3676 -r 4c4e812a67a2 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Nov 01 10:34:34 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="eigen2" version="2.0.17">
-        <repository changeset_revision="a270fba04f3a" name="package_eigen_2_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="confab" version="1.0.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://github.com/bgruening/confab/archive/1.0.1.tar.gz</action>
-
-                <!-- populate the environment variables from the dependend repos -->
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="a270fba04f3a" name="package_eigen_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="eigen2" version="2.0.17" />
-                    </repository>
-                </action>
-
-                <action type="shell_command">cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN2_INCLUDE_DIR=$EIGEN2_SOURCE_PATH</action>
-                <action type="shell_command">make</action>
-                <action type="shell_command">make install</action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="set_to" name="BABEL_DATADIR">$INSTALL_DIR/share/openbabel</environment_variable>
-                    <environment_variable action="set_to" name="BABEL_LIBDIR">$INSTALL_DIR/lib/openbabel/2.2.99</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling Confab requires g++, CMake 2.4+. Optional but required for a few features is libxml2 and zlib.</readme>
-    </package>
-</tool_dependency>