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changeset 24:e8462e1fb27e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit 573c8fb0102ba3ab52fd998494a1b4be3e440620
author bgruening
date Sun, 22 May 2016 18:43:28 -0400
parents d323837e346d
children 9d019ccaa0e3
files confab.tar.bz2 confab.xml repository_dependencies.xml test-data/confab_on_CID_3033.sdf tool_dependencies.xml
diffstat 5 files changed, 293 insertions(+), 28 deletions(-) [+]
line wrap: on
line diff
Binary file confab.tar.bz2 has changed
--- a/confab.xml	Sun Nov 01 10:33:40 2015 -0500
+++ b/confab.xml	Sun May 22 18:43:28 2016 -0400
@@ -1,20 +1,23 @@
-<tool id="ctb_confab" name="Conformer calculation" version="0.1">
+<tool id="ctb_confab" name="Conformer calculation" version="0.3">
     <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="2.3.90dev7d621d9">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}"/>
@@ -33,8 +37,8 @@
             <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='first_conformer' value="True" />
+            <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="4"/>
         </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>
--- a/repository_dependencies.xml	Sun Nov 01 10:33:40 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="8714f927a6ee" name="molecule_datatypes" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/confab_on_CID_3033.sdf	Sun May 22 18:43:28 2016 -0400
@@ -0,0 +1,270 @@
+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
+
+$$$$
--- a/tool_dependencies.xml	Sun Nov 01 10:33:40 2015 -0500
+++ b/tool_dependencies.xml	Sun May 22 18:43:28 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="eigen2" version="2.0.17">
-        <repository changeset_revision="08253ca817b7" name="package_eigen_2_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="53adc55e10f2" name="package_eigen_2_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="confab" version="1.0.1">
         <install version="1.0">
@@ -10,7 +10,7 @@
 
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="08253ca817b7" name="package_eigen_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="53adc55e10f2" name="package_eigen_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="eigen2" version="2.0.17" />
                     </repository>
                 </action>